1
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Pandey R, Urbanc B. Oligomer Formation by Physiologically Relevant C-Terminal Isoforms of Amyloid β-Protein. Biomolecules 2024; 14:774. [PMID: 39062488 PMCID: PMC11274879 DOI: 10.3390/biom14070774] [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: 05/23/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Alzheimer's disease (AD) is a neurological disorder associated with amyloid β-protein (Aβ) assembly into toxic oligomers. In addition to the two predominant alloforms, Aβ1-40 and Aβ1-42, other C-terminally truncated Aβ peptides, including Aβ1-38 and Aβ1-43, are produced in the brain. Here, we use discrete molecular dynamics (DMD) and a four-bead protein model with amino acid-specific hydropathic interactions, DMD4B-HYDRA, to examine oligomer formation of Aβ1-38, Aβ1-40, Aβ1-42, and Aβ1-43. Self-assembly of 32 unstructured monomer peptides into oligomers is examined using 32 replica DMD trajectories for each of the four peptides. In a quasi-steady state, Aβ1-38 and Aβ1-40 adopt similar unimodal oligomer size distributions with a maximum at trimers, whereas Aβ1-42 and Aβ1-43 oligomer size distributions are multimodal with the dominant maximum at trimers or tetramers, and additional maxima at hexamers and unidecamers (for Aβ1-42) or octamers and pentadecamers (for Aβ1-43). The free energy landscapes reveal isoform- and oligomer-order specific structural and morphological features of oligomer ensembles. Our results show that oligomers of each of the four isoforms have unique features, with Aβ1-42 alone resulting in oligomers with disordered and solvent-exposed N-termini. Our findings help unravel the structure-function paradigm governing oligomers formed by various Aβ isoforms.
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Affiliation(s)
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA;
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2
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Mallesh R, Khan J, Gharai PK, Arshi MU, Garg S, Gupta S, Ghosh S. Hydrophobic C-Terminal Peptide Analog Aβ 31-41 Protects the Neurons from Aβ-Induced Toxicity. ACS Chem Neurosci 2024; 15:2372-2385. [PMID: 38822790 DOI: 10.1021/acschemneuro.4c00032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2024] Open
Abstract
Spontaneous aggregation of amyloid beta (Aβ) leads to the formation of neurotoxic senile plaque considered as the most crucial event in Alzheimer's disease (AD) progression. Inhibition or disruption of this deadly aggregate formation is one of the most efficient strategies for the development of potential therapeutics, and extensive research is in progress by various research groups. In this direction, the development of a peptide analogous to that of the native Aβ peptide is an attractive strategy. Based on this rationale, β-sheet breakers were developed from the Aβ central hydrophobic core. These peptide derivatives will bind to the full length of the parent Aβ and interfere in self-recognition, thereby preventing the folding of the Aβ peptide into cross β-sheet neurotoxic aggregates. However, this approach is effective in the inhibition of fibrillar aggregation, but this strategy is ineffective in the Aβ neurotoxic oligomer formation. Therefore, an alternative and efficient approach is to use the Aβ peptide analogous to the C-terminal region, which arbitrates fibrillation and oligomerization. Herein, we developed the Aβ C-terminal fragment (ACT-1 to ACT-7) for inhibition of oligomerization as well as fibrillar aggregation. Screening of these seven peptides resulted in an efficient anti-Aβ peptide aggregative agent (ACT-7), which was evaluated by the ThT assay peptide. The ThT assay reveals complete inhibition and showed significant neuroprotection of PC-12-derived neurons from Aβ-induced toxicity and reduced cell apoptosis. Further, analysis using CD and FTIR spectroscopy reveals that the ACT-7 peptide efficiently inhibits the formation of the β-sheet secondary structure content. HR-TEM microscopic analysis confirmed the inhibition of formation. Therefore, the inhibition of β-sheet Aβ fibrillary aggregation by the protease-stable ACT-7 peptide may provide a beneficial effect on AD treatment to control the Aβ aggregates. Finally, we anticipate that our newly designed ACT peptides may also assist as a template molecular scaffold for designing potential anti-AD therapeutics.
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Affiliation(s)
- Rathnam Mallesh
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Jodhpur, Rajasthan 342037, India
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, WB 700 032, India
- National Institute of Pharmaceutical Education and Research, Kolkata, Chunilal Bhawan 168, Maniktala Main Road, Kolkata 700054, India
| | - Juhee Khan
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Jodhpur, Rajasthan 342037, India
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, WB 700 032, India
| | - Prabir Kumar Gharai
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Jodhpur, Rajasthan 342037, India
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, WB 700 032, India
| | - Mohammad Umar Arshi
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Jodhpur, Rajasthan 342037, India
| | - Shubham Garg
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Jodhpur, Rajasthan 342037, India
| | - Sanju Gupta
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Jodhpur, Rajasthan 342037, India
| | - Surajit Ghosh
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, NH 65, Surpura Bypass Road, Karwar, Jodhpur, Rajasthan 342037, India
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, WB 700 032, India
- National Institute of Pharmaceutical Education and Research, Kolkata, Chunilal Bhawan 168, Maniktala Main Road, Kolkata 700054, India
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3
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Kaur A, Goyal B. Identification of new pentapeptides as potential inhibitors of amyloid-β 42 aggregation using virtual screening and molecular dynamics simulations. J Mol Graph Model 2023; 124:108558. [PMID: 37390790 DOI: 10.1016/j.jmgm.2023.108558] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/02/2023]
Abstract
Alzheimer's disease (AD) is a multifactorial neurodegenerative disease mainly characterized by extracellular accumulation of amyloid-β (Aβ) peptide. Previous studies reported pentapeptide RIIGL as an effective inhibitor of Aβ aggregation and neurotoxicity induced by Aβ aggregates. In this work, a library of 912 pentapeptides based on RIIGL has been designed and assessed for their efficacy to inhibit Aβ42 aggregation using computational techniques. The top hit pentapeptides revealed by molecular docking were further assessed for their binding affinity with Aβ42 monomer using MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) method. The MM-PBSA analysis identified RLAPV, RVVPI, and RIAPA, which bind to Aβ42 monomer with a higher binding affinity -55.80, -46.32, and -44.26 kcal/mol, respectively, as compared to RIIGL (ΔGbinding = -41.29 kcal/mol). The residue-wise binding free energy predicted hydrophobic contacts between Aβ42 monomer and pentapeptides. The secondary structure analysis of the conformational ensembles generated by molecular dynamics (MD) depicted remarkably enhanced sampling of helical and no β-sheet conformations in Aβ42 monomer on the incorporation of RVVPI and RIAPA. Notably, RVVPI and RIAPA destabilized the D23-K28 salt bridge in Aβ42 monomer, which plays a crucial role in Aβ42 oligomer stability and fibril formation. The MD simulations highlighted that the incorporation of proline and arginine in pentapeptides contributed to their strong binding with Aβ42 monomer. Furthermore, RVVPI and RIAPA prevented conformational conversion of Aβ42 monomer to aggregation-prone structures, which, in turn, resulted in a lower aggregation tendency of Aβ42 monomer.
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Affiliation(s)
- Apneet Kaur
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India.
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4
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Arsito PN, Waiwut P, Yenjai C, Arthan S, Monthakantirat O, Nualkaew N, Takomthong P, Boonyarat C. Multifunctional effect of flavonoids from Millettia brandisiana against Alzheimer's disease pathogenesis. Heliyon 2023; 9:e21894. [PMID: 38106662 PMCID: PMC10722324 DOI: 10.1016/j.heliyon.2023.e21894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/07/2023] [Accepted: 10/31/2023] [Indexed: 12/19/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by cognitive impairment and neuronal death. Fifteen flavonoids from Millettia brandisiana were evaluated for the multifunctional effect against AD pathogenesis, including butyrylcholine esterase (BuChE) inhibition, anti-amyloid beta (Aβ) aggregation and neuroprotection against hydrogen peroxide (H2O2) toxicity in differentiated human neuroblastoma SH-SY5Y cell. To understand the mechanism and structure-activity relationship, binding interactions between flavonoids and the BuChE and Aβ were investigated in silico. Furthermore, drug-likeness properties and ADMET parameters were evaluated in silico using SwissADME and pKCSM tools. All flavonoids exhibit a good drug-likeness profile. Six flavonoids have potency in BuChE inhibition, and four flavonoids show potency in anti-Aβ aggregation. Flavonoids with the 6″,6″-dimethylchromeno- [2″,3″:7,8]-flavone structure show a favorable multifunctional effect. In silico analysis showed that flavonoids can bind in various positions to the catalytic triad, anionic site, and acyl pocket. In Aβ1-42, potential flavonoids can attach to the central hydrophobic region and the C terminal hydrophobic and interfere with Aβ interchain hydrogen binding. When compared together, it can inhibit multifunctional action with a favorable ADMET parameter and drug-likeness profile. In addition, candidine can prevent neuronal damage in differentiated SH-SY5Y neuroblastoma cells induced by H2O2 in a dose-dependent manner.
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Affiliation(s)
- Puguh Novi Arsito
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
- School of Pharmacy, Faculty of Medicine and Health Sciences, Universitas Muhammadiyah Yogyakarta, Yogyakarta, 55183, Indonesia
| | - Pornthip Waiwut
- Faculty of Pharmaceutical Sciences, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Chavi Yenjai
- Natural Products Research Unit, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Supakorn Arthan
- Program of Chemistry, Faculty of Science and Technology, Sakon Nakhon Rajabhat University, Mueang District, Sakon Nakhon, 47000, Thailand
| | - Orawan Monthakantirat
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Natsajee Nualkaew
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
| | | | - Chantana Boonyarat
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
- Center for Research and Development of Herbal Health Products, Khon Kaen University, Khon Kaen, 40002, Thailand
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5
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Taha HB, Chawla E, Bitan G. IM-MS and ECD-MS/MS Provide Insight into Modulation of Amyloid Proteins Self-Assembly by Peptides and Small Molecules. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2066-2086. [PMID: 37607351 DOI: 10.1021/jasms.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Neurodegenerative proteinopathies are characterized by formation and deposition of misfolded, aggregated proteins in the nervous system leading to neuronal dysfunction and death. It is widely believed that metastable oligomers of the offending proteins, preceding the fibrillar aggregates found in the tissue, are the proximal neurotoxins. There are currently almost no disease-modifying therapies for these diseases despite an active pipeline of preclinical development and clinical trials for over two decades, largely because studying the metastable oligomers and their interaction with potential therapeutics is notoriously difficult. Mass spectrometry (MS) is a powerful analytical tool for structural investigation of proteins, including protein-protein and protein-ligand interactions. Specific MS tools have been useful in determining the composition and conformation of abnormal protein oligomers involved in proteinopathies and the way they interact with drug candidates. Here, we analyze critically the utilization of ion-mobility spectroscopy-MS (IM-MS) and electron-capture dissociation (ECD) MS/MS for analyzing the oligomerization and conformation of multiple amyloidogenic proteins. We also discuss IM-MS investigation of their interaction with two classes of compounds developed by our group over the last two decades: C-terminal fragments derived from the 42-residue form of amyloid β-protein (Aβ42) and molecular tweezers. Finally, we review the utilization of ECD-MS/MS for elucidating the binding sites of the ligands on multiple proteins. These approaches are readily applicable to future studies addressing similar questions and hold promise for facilitating the development of successful disease-modifying drugs against neurodegenerative proteinopathies.
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Affiliation(s)
- Hash Brown Taha
- Department of Neurology, University of California Los Angeles, California 90095, United States
- Department of Integrative Biology & Physiology, University of California Los Angeles, California 90095, United States
| | - Esha Chawla
- Department of Neurology, University of California Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, California 90095, United States
| | - Gal Bitan
- Department of Neurology, University of California Los Angeles, California 90095, United States
- Brain Research Institute, University of California Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California Los Angeles, California 90095, United States
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6
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Bhopatkar AA, Kayed R. Flanking regions, amyloid cores, and polymorphism: the potential interplay underlying structural diversity. J Biol Chem 2023; 299:105122. [PMID: 37536631 PMCID: PMC10482755 DOI: 10.1016/j.jbc.2023.105122] [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: 04/26/2023] [Revised: 07/10/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023] Open
Abstract
The β-sheet-rich amyloid core is the defining feature of protein aggregates associated with neurodegenerative disorders. Recent investigations have revealed that there exist multiple examples of the same protein, with the same sequence, forming a variety of amyloid cores with distinct structural characteristics. These structural variants, termed as polymorphs, are hypothesized to influence the pathological profile and the progression of different neurodegenerative diseases, giving rise to unique phenotypic differences. Thus, identifying the origin and properties of these structural variants remain a focus of studies, as a preliminary step in the development of therapeutic strategies. Here, we review the potential role of the flanking regions of amyloid cores in inducing polymorphism. These regions, adjacent to the amyloid cores, show a preponderance for being structurally disordered, imbuing them with functional promiscuity. The dynamic nature of the flanking regions can then manifest in the form of conformational polymorphism of the aggregates. We take a closer look at the sequences flanking the amyloid cores, followed by a review of the polymorphic aggregates of the well-characterized proteins amyloid-β, α-synuclein, Tau, and TDP-43. We also consider different factors that can potentially influence aggregate structure and how these regions can be viewed as novel targets for therapeutic strategies by utilizing their unique structural properties.
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Affiliation(s)
- Anukool A Bhopatkar
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, USA.
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7
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Dey P, Biswas P. Exploring the aggregation of amyloid-β 42 through Monte Carlo simulations. Biophys Chem 2023; 297:107011. [PMID: 37037120 DOI: 10.1016/j.bpc.2023.107011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/25/2023] [Accepted: 03/26/2023] [Indexed: 04/09/2023]
Abstract
Coarse-grained Monte Carlo simulations are performed for a disordered protein, amyloid-β 42 to identify the interactions and understand the mechanism of its aggregation. A statistical potential is developed from a selected dataset of intrinsically disordered proteins, which accounts for the respective contributions of the bonded and non-bonded potentials. While, the bonded potential comprises the bond, bend, and dihedral constraints, the nonbonded interactions include van der Waals interactions, hydrogen bonds, and the two-body potential. The two-body potential captures the features of both hydrophobic and electrostatic interactions that brings the chains at a contact distance, while the repulsive van der Waals interactions prevent them from a collapse. Increased two-body hydrophobic interactions facilitate the formation of amorphous aggregates rather than the fibrillar ones. The formation of aggregates is validated from the interchain distances, and the total energy of the system. The aggregate is structurally characterized by the root-mean-square deviation, root-mean-square fluctuation and the radius of gyration. The aggregates are characterized by a decrease in SASA, an increase in the non-local interactions and a distinct free energy minimum relative to that of the monomeric state of amyloid-β 42. The hydrophobic residues help in nucleation, while the charged residues help in oligomerization and aggregation.
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8
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Fang M, Su K, Wang X, Guan P, Hu X. Study on molecular mechanisms of destabilizing Aβ(1-42) protofibrils by licochalcone A and licochalcone B using molecular dynamics simulations. J Mol Graph Model 2023; 122:108500. [PMID: 37094420 DOI: 10.1016/j.jmgm.2023.108500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/30/2023] [Accepted: 04/17/2023] [Indexed: 04/26/2023]
Abstract
Amyloid-beta (Aβ) protofibrils are closely related to Alzheimer's disease. Their behaviors with or without the presence of Aβ fibrillization inhibitors have been intensively studied by molecular dynamics simulations. In this work, the molecular mechanisms of licochalcone A and licochalcone B on destabilizing Aβ(1-42) protofibrils are explored. It is found that both two licochalcones can disorder the configuration of the Aβ(1-42) protofibril. The stable interactions between the Aβ(1-42) protofibril and licochalcone A or licochalcone B are able to be formed. A reduction of the β-sheet structure contents and an increment of the random coil structures of Aβ(1-42) protofibril are observed in the presence of either licochalcone A or licochalcone B. The hydrogen bonds inside the Aβ(1-42) protofibril could be partially collapsed to varying degrees by two licochalcones. Furthermore, the van der Waals interactions between Aβ(1-42) protofibril and licochalcone A make an important contribution to the binding free energy, while the contribution of the electrostatic interactions between Aβ(1-42) protofibril and licochalcone B is more prominent in the binding affinity. Our work may help in the development of new drug candidates for disrupting the Aβ protofibril.
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Affiliation(s)
- Mei Fang
- Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China.
| | - Kehe Su
- Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China
| | - Xin Wang
- Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China
| | - Ping Guan
- Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China.
| | - Xiaoling Hu
- Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China.
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9
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Andrews B, Ruggiero T, Urbanc B. How do salt and lipids affect conformational dynamics of Aβ42 monomers in water? Phys Chem Chem Phys 2023; 25:2566-2583. [PMID: 36602150 DOI: 10.1039/d2cp05044g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
It is well established that amyloid β-protein (Aβ) self-assembly is involved in triggering of Alzheimer's disease. On the other hand, evidence of physiological function of Aβ interacting with lipids has only begun to emerge. Details of Aβ-lipid interactions, which may underlie physiological and pathological activities of Aβ, are not well understood. Here, the effects of salt and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids on conformational dynamics of Aβ42 monomer in water are examined by all-atom molecular dynamics (MD). We acquired six sets of 250 ns long MD trajectories for each of the three lipid concentrations (0, 27, and 109 mM) in the absence and presence of 150 mM salt. Ten replica trajectories per set are used to enhance sampling of Aβ42 conformational space. We show that salt facilitates long-range tertiary contacts in Aβ42, resulting in more compact Aβ42 conformations. By contrast, addition of lipids results in lipid-concentration dependent Aβ42 unfolding concomitant with enhanced stability of the turn in the A21-A30 region. At the high lipid concentration, salt enables the N-terminal region of Aβ42 to form long-range tertiary contacts and interact with lipids, which results in formation of a parallel β-strand. Aβ42 forms stable lipid-protein complexes whereby the protein is adhered to the lipid cluster rather than embedded into it. We propose that the inability of Aβ42 monomer to get embedded into the lipid cluster may be important for facilitating repair of leaks in the blood-brain barrier without penetrating and damaging cellular membranes.
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Affiliation(s)
- Brian Andrews
- Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA.
| | - Thomas Ruggiero
- Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA.
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA.
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Xie D, Deng T, Zhai Z, Sun T, Xu Y. The cellular model for Alzheimer's disease research: PC12 cells. Front Mol Neurosci 2023; 15:1016559. [PMID: 36683856 PMCID: PMC9846650 DOI: 10.3389/fnmol.2022.1016559] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/08/2022] [Indexed: 01/06/2023] Open
Abstract
Alzheimer's disease (AD) is a common age-related neurodegenerative disease characterized by progressive cognitive decline and irreversible memory impairment. Currently, several studies have failed to fully elucidate AD's cellular and molecular mechanisms. For this purpose, research on related cellular models may propose potential predictive models for the drug development of AD. Therefore, many cells characterized by neuronal properties are widely used to mimic the pathological process of AD, such as PC12, SH-SY5Y, and N2a, especially the PC12 pheochromocytoma cell line. Thus, this review covers the most systematic essay that used PC12 cells to study AD. We depict the cellular source, culture condition, differentiation methods, transfection methods, drugs inducing AD, general approaches (evaluation methods and metrics), and in vitro cellular models used in parallel with PC12 cells.
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Affiliation(s)
- Danni Xie
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ting Deng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhenwei Zhai
- School of Medical Information Engineering, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tao Sun
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Medical Information Engineering, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ying Xu
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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11
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Puławski W, Dzwolak W. Virtual Quasi-2D Intermediates as Building Blocks for Plausible Structural Models of Amyloid Fibrils from Proteins with Complex Topologies: A Case Study of Insulin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7024-7034. [PMID: 35617668 PMCID: PMC9178918 DOI: 10.1021/acs.langmuir.2c00699] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Conformational transitions of globular proteins into amyloid fibrils are complex multistage processes exceedingly challenging to simulate using molecular dynamics (MD). Slow monomer diffusion rates and rugged free energy landscapes disfavor swift self-assembly of orderly amyloid architectures within timescales accessible to all-atom MD. Here, we conduct a multiscale MD study of the amyloidogenic self-assembly of insulin: a small protein with a complex topology defined by two polypeptide chains interlinked by three disulfide bonds. To avoid kinetic traps, unconventional preplanarized insulin conformations are used as amyloid building blocks. These starting conformers generated through uniaxial compression of the native monomer in various spatial directions represent 6 distinct (out of 16 conceivable) two-dimensional (2D) topological classes varying in N-/C-terminal segments of insulin's A- and B-chains being placed inside or outside of the central loop constituted by the middle sections of both chains and Cys7A-Cys7B/Cys19B-Cys20A disulfide bonds. Simulations of the fibrillar self-assembly are initiated through a biased in-register alignment of two, three, or four layers of flat conformers belonging to a single topological class. The various starting topologies are conserved throughout the self-assembly process resulting in polymorphic amyloid fibrils varying in structural features such as helical twist, presence of cavities, and overall stability. Some of the protofilament structures obtained in this work are highly compatible with the earlier biophysical studies on insulin amyloid and high-resolution studies on insulin-derived amyloidogenic peptide models postulating the presence of steric zippers. Our approach provides in silico means to study amyloidogenic tendencies and viable amyloid architectures of larger disulfide-constrained proteins with complex topologies.
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Affiliation(s)
- Wojciech Puławski
- Institute
of High Pressure Physics, Polish Academy
of Sciences, 29/37 Sokołowska
Str., 01-142 Warsaw, Poland
| | - Wojciech Dzwolak
- Institute
of High Pressure Physics, Polish Academy
of Sciences, 29/37 Sokołowska
Str., 01-142 Warsaw, Poland
- Faculty
of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Str., 02-093 Warsaw, Poland
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12
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Tagad A, Singh RK, Patwari GN. Binary Matrix Method to Enumerate, Hierarchically Order, and Structurally Classify Peptide Aggregation. J Chem Inf Model 2022; 62:1585-1594. [PMID: 35232014 DOI: 10.1021/acs.jcim.2c00069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein aggregation is a common and complex phenomenon in biological processes, yet a robust analysis of this aggregation process remains elusive. The commonly used methods such as center-of-mass to center-of-mass (COM-COM) distance, the radius of gyration (Rg), hydrogen bonding (HB), and solvent accessible surface area do not quantify the aggregation accurately. Herein, a new and robust method that uses an aggregation matrix (AM) approach to investigate peptide aggregation in a MD simulation trajectory is presented. An nxn two-dimensional AM is created by using the interpeptide Cα-Cα cutoff distances, which are binarily encoded (0 or 1). These aggregation matrices are analyzed to enumerate, hierarchically order, and structurally classify the aggregates. Comparison of the present AM method suggests that it is superior to the HB method since it can incorporate nonspecific interactions and the Rg and COM-COM methods since the cutoff distance is independent of the length of the peptide. More importantly, the present method can structurally classify the peptide aggregates, which the conventional Rg, COM-COM, and HB methods fail to do. The unique selling point of this method is its ability to structurally classify peptide aggregates using two-dimensional matrices.
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Affiliation(s)
- Amol Tagad
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Reman Kumar Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - G Naresh Patwari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Chen Y, Li X, Zhan C, Lao Z, Li F, Dong X, Wei G. A Comprehensive Insight into the Mechanisms of Dopamine in Disrupting Aβ Protofibrils and Inhibiting Aβ Aggregation. ACS Chem Neurosci 2021; 12:4007-4019. [PMID: 34472835 DOI: 10.1021/acschemneuro.1c00306] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Fibrillary aggregates of amyloid-β (Aβ) are the pathological hallmark of Alzheimer's disease (AD). Clearing Aβ deposition or inhibiting Aβ aggregation is a promising approach to treat AD. Experimental studies reported that dopamine (DA), an important neurotransmitter, can inhibit Aβ aggregation and disrupt Aβ fibrils in a dose-dependent manner. However, the underlying molecular mechanisms still remain mostly elusive. Herein, we investigated the effect of DA on Aβ42 protofibrils at three different DA-to-Aβ molar ratios (1:1, 2:1, and 10:1) using all-atom molecular dynamics simulations. Our simulations demonstrate that protonated DA at a DA-to-Aβ ratio of 2:1 exhibits stronger Aβ protofibril disruptive capacity than that at a molar-ratio of 1:1 by mostly disrupting the F4-L34-V36 hydrophobic core. When the ratio of DA-to-Aβ increases to 10:1, DA has a high probability to bind to the outer surface of protofibril and has negligible effect on the protofibril structure. Interestingly, at the same DA-to-Aβ ratio (10:1), a mixture of protonated (DA+) and deprotonated (DA0) DA molecules significantly disrupts Aβ protofibrils by the binding of DA0 to the F4-L34-V36 hydrophobic core. Replica-exchange molecular dynamics simulations of Aβ42 dimer show that DA+ inhibits the formation of β-sheets, K28-A42/K28-D23 salt-bridges, and interpeptide hydrophobic interactions and results in disordered coil-rich Aβ dimers, which would inhibit the subsequent fibrillization of Aβ. Further analyses reveal that DA disrupts Aβ protofibril and prevents Aβ dimerization mostly through π-π stacking interactions with residues F4, H6, and H13, hydrogen bonding interactions with negatively charged residues D7, E11, E22 and D23, and cation-π interactions with residues R5. This study provides a complete picture of the molecular mechanisms of DA in disrupting Aβ protofibril and inhibiting Aβ aggregation, which could be helpful for the design of potent drug candidates for the treatment/intervention of AD.
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Affiliation(s)
- Yujie Chen
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People’s Republic of China
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, People’s Republic of China
| | - Chendi Zhan
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People’s Republic of China
| | - Zenghui Lao
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People’s Republic of China
| | - Fangying Li
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People’s Republic of China
| | - Xuewei Dong
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People’s Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People’s Republic of China
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14
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Sorout N, Chandra A. Interactions of the Aβ(1-42) Peptide with Boron Nitride Nanoparticles of Varying Curvature in an Aqueous Medium: Different Pathways to Inhibit β-Sheet Formation. J Phys Chem B 2021; 125:11159-11178. [PMID: 34605235 DOI: 10.1021/acs.jpcb.1c05805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The aggregation of amyloid β (Aβ) peptide triggered by its conformational changes leads to the commonly known neurodegenerative disease of Alzheimer's. It is believed that the formation of β sheets of the peptide plays a key role in its aggregation and subsequent fibrillization. In the current study, we have investigated the interactions of the Aβ(1-42) peptide with boron nitride nanoparticles and the effects of the latter on conformational transitions of the peptide through a series of molecular dynamics simulations. In particular, the effects of curvature of the nanoparticle surface are studied by considering boron nitride nanotubes (BNNTs) of varying diameter and also a planar boron nitride nanosheet (BNNS). Altogether, the current study involves the generation and analysis of 9.5 μs of dynamical trajectories of peptide-BNNT/BNNS pairs in an aqueous medium. It is found that BN nanoparticles of different curvatures that are studied in the present work inhibit the conformational transition of the peptide to its β-sheet form. However, such an inhibition effect follows different pathways for BN nanoparticles of different curvatures. For the BNNT with the highest surface curvature, i.e., (3,3) BNNT, the nanoparticle is found to inhibit β-sheet formation by stabilizing the helical structure of the peptide, whereas for planar BNNS, the β-sheet formation is prevented by making more favorable pathways available for transitions of the peptide to conformations of random coils and turns. The BNNTs with intermediate curvatures are found to exhibit diverse pathways of their interactions with the peptide, but in all cases, essentially no formation of the β sheet is found whereas substantial β-sheet formation is observed for Aβ(1-42) in water in the absence of any nanoparticle. The current study shows that BN nanoparticles have the potential to act as effective tools to prevent amyloid formation from Aβ peptides.
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Affiliation(s)
- Nidhi Sorout
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh, India 208016
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh, India 208016
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Multi-Target Actions of Acridones from Atalantia monophylla towards Alzheimer's Pathogenesis and Their Pharmacokinetic Properties. Pharmaceuticals (Basel) 2021; 14:ph14090888. [PMID: 34577588 PMCID: PMC8470973 DOI: 10.3390/ph14090888] [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: 07/26/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022] Open
Abstract
Ten acridones isolated from Atalantia monophylla were evaluated for effects on Alzheimer’s disease pathogenesis including antioxidant effects, acetylcholinesterase (AChE) inhibition, prevention of beta-amyloid (Aβ) aggregation and neuroprotection. To understand the mechanism, the type of AChE inhibition was investigated in vitro and binding interactions between acridones and AChE or Aβ were explored in silico. Drug-likeness and ADMET parameters were predicted in silico using SwissADME and pKCSM programs, respectively. All acridones showed favorable drug-likeness and possessed multifunctional activities targeting AChE function, Aβ aggregation and oxidation. All acridones inhibited AChE in a mixed-type manner and bound AChE at both catalytic anionic and peripheral anionic sites. In silico analysis showed that acridones interfered with Aβ aggregation by interacting at the central hydrophobic core, C-terminal hydrophobic region, and the key residues 41 and 42. Citrusinine II showed potent multifunctional action with the best ADMET profile and could alleviate neuronal cell damage induced by hydrogen peroxide and Aβ1-42 toxicity.
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16
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Andrews B, Long K, Urbanc B. Soluble State of Villin Headpiece Protein as a Tool in the Assessment of MD Force Fields. J Phys Chem B 2021; 125:6897-6911. [PMID: 34143637 DOI: 10.1021/acs.jpcb.1c04589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protein self-assembly plays an important role in cellular processes. Whereas molecular dynamics (MD) represents a powerful tool in studying assembly mechanisms, its predictions depend on the accuracy of underlying force fields, which are known to overly promote protein assembly. We here examine villin headpiece domain, HP36, which remains soluble at concentrations amenable to MD studies. The experimental characterization of soluble HP36 at concentrations of 0.05 to 1 mM reveals concentration-independent 90% monomeric and 10% dimeric populations. Extensive all-atom MD simulations at two protein concentrations, 0.9 and 8.5 mM, probe the HP36 dimer population, stability, and kinetics of dimer formation within two MD force fields, Amber ff14SB and CHARMM36m. MD results demonstrate that whereas CHARMM36m captures experimental HP36 monomer populations at the lower concentration, both force fields overly promote HP36 association at the higher concentration. Moreover, contacts stabilizing HP36 dimers are force-field-dependent. CHARMM36m produces consistently higher HP36 monomer populations, lower association rates, and weaker dependence of these quantities on the protein concentration than Amber ff14SB. Nonetheless, the highest monomer populations and dissociation constants are observed when the TIP3P water model in Amber ff14SB is replaced by TIP4P/2005, showcasing the critical role of the water model in addressing the protein solubility problem in MD.
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Affiliation(s)
- Brian Andrews
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Kaho Long
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
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Raskatov JA, Schneider JP, Nilsson BL. Defining the Landscape of the Pauling-Corey Rippled Sheet: An Orphaned Motif Finding New Homes. Acc Chem Res 2021; 54:2488-2501. [PMID: 33901396 PMCID: PMC8154201 DOI: 10.1021/acs.accounts.1c00084] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
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When peptides are mixed with their mirror images in an equimolar
ratio, two-dimensional periodic structural folds can form, in which
extended peptide strands are arrayed with alternating chirality. The
resultant topography class, termed the rippled β-sheet, was
introduced as a theoretical concept by Pauling and Corey in 1953.
Unlike other fundamental protein structural motifs identified around
that time, including the α-helix and the pleated β-sheet,
it took several decades before conclusive experimental data supporting
the proposed rippled β-sheet motif were gained. Much of the
key experimental evidence was provided over the course of the past
decade through the concurrent efforts of our three laboratories. Studies
that focused on developing new self-assembling hydrogel materials
have shown that certain amphiphilic peptides form fibrils and hydrogel
networks that are more rigid and have a higher thermodynamic stability
when made from racemic peptide mixtures as opposed to pure enantiomers.
Related interrogation of assemblies composed of mixtures of l- and d-amphiphilic peptides confirmed that the resulting
fibrils were composed of alternating l/d peptides
consistent with rippled β-sheets. It was also demonstrated that
mirror-image amyloid beta (Aβ) could act as a molecular chaperone
to promote oligomer-to-fibril conversion of the natural Aβ enantiomer,
which was found to reduce Aβ neurotoxicity against different
neuronal cell models. With a cross-disciplinary approach that combines
experiment and theory, our three laboratories have demonstrated the
unique biophysical, biochemical, and biological properties that arise
upon mixing of peptide enantiomers, in consequence of rippled β-sheet
formation. In this Account, we give an overview of the early history
of the rippled β-sheet and provide a detailed structural description/definition
of this motif relative to the pleated β-sheet. We then summarize
the key findings, obtained on three unique sets of aggregating mirror-image
peptide pairs through independent efforts of our three laboratories,
and use these results to delineate the landscape of the rippled β-sheet
structural motif to inspire future studies. Peptide sequence parameters
that favor rippled β-sheet assembly are described, along with
the accompanying kinetic and thermodynamic properties, as well as
the resulting emergent physical properties of the assemblies. The
Account then concludes with a brief overview of some key unresolved
challenges in this nascent field. There is much potential for future
applications of this unique supramolecular motif in the realm of materials
design and biomedical research. We hope this Account will stimulate
much-needed discussion of this fascinating structural class to eventually
produce a fully quantitative, rational framework for the molecular
engineering of rippled β-sheets in the future.
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Affiliation(s)
- Jevgenij A. Raskatov
- Department of Chemistry and Biochemistry, UCSC, 1156 High Street, Santa Cruz, California 95064, United States
| | - Joel P. Schneider
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Bradley L. Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
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Limegrover CS, LeVine H, Izzo NJ, Yurko R, Mozzoni K, Rehak C, Sadlek K, Safferstein H, Catalano SM. Alzheimer's protection effect of A673T mutation may be driven by lower Aβ oligomer binding affinity. J Neurochem 2021; 157:1316-1330. [PMID: 33025581 PMCID: PMC8246829 DOI: 10.1111/jnc.15212] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/16/2022]
Abstract
Several mutations conferring protection against Alzheimer's disease (AD) have been described, none as profound as the A673T mutation, where carriers are four times less likely to get AD compared to noncarriers. This mutation results in reduced amyloid beta (Aβ) protein production in vitro and lower lifetime Aβ concentration in carriers. Better understanding of the protective mechanisms of the mutation may provide important insights into AD pathophysiology and identify productive therapeutic intervention strategies for disease modification. Aβ(1-42) protein forms oligomers that bind saturably to a single receptor site on neuronal synapses, initiating the downstream toxicities observed in AD. Decreased formation, toxicity, or stability of soluble Aβ oligomers, or reduction of synaptic binding of these oligomers, may combine with overall lower Aβ concentration to underlie A673T's disease protecting mechanism. To investigate these possibilities, we compared the formation rate of soluble oligomers made from Icelandic A673T mutant and wild type (wt) Aβ(1-42) synthetic protein, the amount and intensity of oligomer bound to mature primary rat hippocampal/cortical neuronal synapses, and the potency of bound oligomers to impact trafficking rate in neurons in vitro using a physiologically relevant oligomer preparation method. At equal protein concentrations, mutant protein forms approximately 50% or fewer oligomers of high molecular weight (>50 kDa) compared to wt protein. Mutant oligomers are twice as potent at altering the cellular vesicle trafficking rate as wt at equivalent concentrations, however, mutant oligomers have a >4-fold lower binding affinity to synaptic receptors (Kd = 1,950 vs. 442 nM). The net effect of these differences is a lower overall toxicity at a given concentration. This study demonstrates for the first time that mutant A673T Aβ oligomers prepared with this method have fundamentally different assembly characteristics and biological impact from wt protein and indicates that its disease protecting mechanism may result primarily from the mutant protein's much lower binding affinity to synaptic receptors. This suggests that therapeutics that effectively reduce oligomer binding to synapses in the brain may be beneficial in AD.
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Affiliation(s)
| | - Harry LeVine
- Sanders‐Brown Center on AgingUniversity of KentuckyLexingtonKYUSA
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Tangrodchanapong T, Sornkaew N, Yurasakpong L, Niamnont N, Nantasenamat C, Sobhon P, Meemon K. Beneficial Effects of Cyclic Ether 2-Butoxytetrahydrofuran from Sea Cucumber Holothuria scabra against Aβ Aggregate Toxicity in Transgenic Caenorhabditis elegans and Potential Chemical Interaction. Molecules 2021; 26:molecules26082195. [PMID: 33920352 PMCID: PMC8070609 DOI: 10.3390/molecules26082195] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 12/24/2022] Open
Abstract
The pathological finding of amyloid-β (Aβ) aggregates is thought to be a leading cause of untreated Alzheimer’s disease (AD). In this study, we isolated 2-butoxytetrahydrofuran (2-BTHF), a small cyclic ether, from Holothuria scabra and demonstrated its therapeutic potential against AD through the attenuation of Aβ aggregation in a transgenic Caenorhabditis elegans model. Our results revealed that amongst the five H. scabra isolated compounds, 2-BTHF was shown to be the most effective in suppressing worm paralysis caused by Aβ toxicity and in expressing strong neuroprotection in CL4176 and CL2355 strains, respectively. An immunoblot analysis showed that CL4176 and CL2006 treated with 2-BTHF showed no effect on the level of Aβ monomers but significantly reduced the toxic oligomeric form and the amount of 1,4-bis(3-carboxy-hydroxy-phenylethenyl)-benzene (X-34)-positive fibril deposits. This concurrently occurred with a reduction of reactive oxygen species (ROS) in the treated CL4176 worms. Mechanistically, heat shock factor 1 (HSF-1) (at residues histidine 63 (HIS63) and glutamine 72 (GLN72)) was shown to be 2-BTHF’s potential target that might contribute to an increased expression of autophagy-related genes required for the breakdown of the Aβ aggregate, thus attenuating its toxicity. In conclusion, 2-BTHF from H. scabra could protect C. elegans from Aβ toxicity by suppressing its aggregation via an HSF-1-regulated autophagic pathway and has been implicated as a potential drug for AD.
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Affiliation(s)
- Taweesak Tangrodchanapong
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (T.T.); (L.Y.); (P.S.)
| | - Nilubon Sornkaew
- Department of Chemistry, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand; (N.S.); (N.N.)
| | - Laphatrada Yurasakpong
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (T.T.); (L.Y.); (P.S.)
| | - Nakorn Niamnont
- Department of Chemistry, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand; (N.S.); (N.N.)
| | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand;
| | - Prasert Sobhon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (T.T.); (L.Y.); (P.S.)
| | - Krai Meemon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (T.T.); (L.Y.); (P.S.)
- Correspondence: or ; Tel.: +66-22-015-407
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20
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Zhu J, Su T, Wang M, Li M, Liu L, Wang F. Highly Expressed Amyloid Beta-42 Of Aqueous Humor In Patients With Neovascular Macular Degeneration. Semin Ophthalmol 2021; 36:9-13. [PMID: 33587673 DOI: 10.1080/08820538.2021.1883679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Background: Age-related macular degeneration (AMD) is a type of macular degeneration disease, and amyloid beta (aβ) is the main component of vitreous warts in AMD patients. Neovascular AMD (nAMD) is the most serious type of AMD, but its pathogenesis remains unclear. The aim of this study was to detect the expression of aβ42 in the aqueous humor of nAMD patients and to evaluate whether aβ42 expression of aqueous humor is correlated with cognitive function in these patients.Methods: A total of 70 patients were enrolled in this study, including 50 nAMD patients (nAMD group) and 20 patients with cataract (control group). The cognitive function of the patients was assessed using the Mini-Mental State Examination and Montreal Cognitive Assessment Scale, and based on their scores, 50 patients with nAMD were divided into two subgroups: the p-nAMD group (18 nAMD patients with normal cognition) and the ci-nAMD group (32 nAMD patients with cognitive impairment). An immunofluorescence microsphere probe technique was used to detect the aβ42 expression of aqueous humor in all patients. Pearson correlation analysis was used.Results: The aβ42 expression of aqueous humor was significantly higher in the nAMD group (124.56 ± 41.93 pg/mL) as compared with the control group (82.94 ± 33.75 pg/mL; P < .01). There was no significant difference in aβ42 expression of aqueous humor between the p-nAMD group (136.42 ± 51.68 pg/mL) and ci-nAMD group (117.90 ± 34.46 pg/mL; P = .14).Conclusion: In nAMD patients, aβ42 was highly expressed in the aqueous humor but was not correlated with cognitive function.
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Affiliation(s)
- Juming Zhu
- Department of Ophthalmology, the Fourth Affiliated Hospital of Nantong University, Yancheng No.1 People's Hospital, Yancheng, Jiangsu Province, China
| | - Tu Su
- Department of Ophthalmology, Shanghai Tenth People's Hospital, Affiliate of Tongji University, School of Medicine, Shanghai, China
| | - Minli Wang
- Department of Ophthalmology, Shanghai Tenth People's Hospital, Affiliate of Tongji University, School of Medicine, Shanghai, China
| | - Min Li
- Department of Ophthalmology, Shanghai Tenth People's Hospital, Affiliate of Tongji University, School of Medicine, Shanghai, China
| | - Lin Liu
- Department of Ophthalmology, Shanghai Tenth People's Hospital, Affiliate of Tongji University, School of Medicine, Shanghai, China
| | - Fang Wang
- Department of Ophthalmology, Shanghai Tenth People's Hospital, Affiliate of Tongji University, School of Medicine, Shanghai, China
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21
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Zhang Y, Tang Y, Zhang D, Liu Y, He J, Chang Y, Zheng J. Amyloid cross-seeding between Aβ and hIAPP in relation to the pathogenesis of Alzheimer and type 2 diabetes. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.09.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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22
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Aggarwal L, Biswas P. Hydration Thermodynamics of the N-Terminal FAD Mutants of Amyloid-β. J Chem Inf Model 2021; 61:298-310. [PMID: 33440932 DOI: 10.1021/acs.jcim.0c01286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hydration thermodynamics of amyloid-β (Aβ) and its pathogenic familial Alzheimer's disease (FAD) mutants such as A2V, Taiwan (D7H), Tottori (D7N), and English (H6R) and the protective A2T mutant is investigated by a combination of all-atom, explicit water molecular dynamics (MD) simulations and the three-dimensional reference interaction site model (3D-RISM) theory. The change in the hydration free energy on mutation is decomposed into the energetic and entropic components, which comprise electrostatic and nonelectrostatic contributions. An increase in the hydration free energy is observed for A2V, D7H, D7N, and H6R mutations that increase the aggregation propensity of Aβ and lead to an early onset of Alzheimer's disease, while a reverse trend is noted for the protective A2T mutation. An antiphase correlation is found between the change in the hydration energy and the internal energy of Aβ upon mutation. A residue-wise decomposition analysis shows that the change in the hydration free energy of Aβ on mutation is primarily due to the hydration/dehydration of the side-chain atoms of the negatively charged residues. The decrease in the hydration of the negatively charged residues on mutation may decrease the solubility of the mutant, which increases the observed aggregation propensity of the FAD mutants. Results obtained from the theory show an excellent match with the experimentally reported data.
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Affiliation(s)
- Leena Aggarwal
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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23
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Urbanc B. Cross-Linked Amyloid β-Protein Oligomers: A Missing Link in Alzheimer's Disease Pathology? J Phys Chem B 2021; 125:1307-1316. [PMID: 33440940 DOI: 10.1021/acs.jpcb.0c07716] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Amyloid β-protein (Aβ) oligomers are broadly viewed as the proximate mediators of toxicity in Alzheimer's disease (AD). Recent studies, however, provide substantial evidence that Aβ is involved in protection and repair of the central nervous system whereby Aβ oligomer and subsequent fibril formation are integral to its normal antimicrobial and antiviral function. These developments raise a question of what exactly makes Aβ oligomers toxic in the context of AD. This Perspective describes a paradigm shift in the search for toxic Aβ oligomer species that involves oxidative-stress-induced stabilization of Aβ oligomers via cross-linking and reviews most recent research elucidating structural aspects of cross-linked Aβ oligomers and potential inhibition of their toxicity.
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Affiliation(s)
- Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
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24
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Tandem-Homodimer of a β-Sheet-Forming Short Peptide Inhibits Random-to-β Structural Transition of Its Original Monomer. Processes (Basel) 2020. [DOI: 10.3390/pr8111421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
There is an increasing interest in designing fibrillogenesis modulators for treating amyloid β (Aβ)-peptide-associated diseases. The use of Aβ fragment peptides and their derivatives, as well as nonpeptidyl natural products, is one promising approach to prevent Aβ fibrillation. In this study, we demonstrate that tandem-homodimers (TDs) of a β-sheet-forming short peptide in which the amino acid sequence is duplicated in series and joined via an amino alkanoic acid linker of different chain lengths, preventing the random-to-β structural transition of the original monomer. Ape5-TD, containing 5-amino pentanoate, most potently prevented this transition for at least five days by generating disordered aggregates with reduced tryptic stability. The linkers in the TDs generated this inhibitory activity, probably due to their bent conformations and hydrophobicity, appropriate for accommodating and twisting the monomers, resulting in irregular arrangements of the peptides. The present study could allow the design of a new class of protein/peptide fibrillogenesis modulators.
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Tangrodchanapong T, Sobhon P, Meemon K. Frondoside A Attenuates Amyloid-β Proteotoxicity in Transgenic Caenorhabditis elegans by Suppressing Its Formation. Front Pharmacol 2020; 11:553579. [PMID: 33013392 PMCID: PMC7513805 DOI: 10.3389/fphar.2020.553579] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/24/2020] [Indexed: 11/16/2022] Open
Abstract
Oligomeric assembly of Amyloid-β (Aβ) is the main toxic species that contribute to early cognitive impairment in Alzheimer’s patients. Therefore, drugs that reduce the formation of Aβ oligomers could halt the disease progression. In this study, by using transgenic Caenorhabditis elegans model of Alzheimer’s disease, we investigated the effects of frondoside A, a well-known sea cucumber Cucumaria frondosa saponin with anti-cancer activity, on Aβ aggregation and proteotoxicity. The results showed that frondoside A at a low concentration of 1 µM significantly delayed the worm paralysis caused by Aβ aggregation as compared with control group. In addition, the number of Aβ plaque deposits in transgenic worm tissues was significantly decreased. Frondoside A was more effective in these activities than ginsenoside-Rg3, a comparable ginseng saponin. Immunoblot analysis revealed that the level of small oligomers as well as various high molecular weights of Aβ species in the transgenic C. elegans were significantly reduced upon treatment with frondoside A, whereas the level of Aβ monomers was not altered. This suggested that frondoside A may primarily reduce the level of small oligomeric forms, the most toxic species of Aβ. Frondoside A also protected the worms from oxidative stress and rescued chemotaxis dysfunction in a transgenic strain whose neurons express Aβ. Taken together, these data suggested that low dose of frondoside A could protect against Aβ-induced toxicity by primarily suppressing the formation of Aβ oligomers. Thus, the molecular mechanism of how frondoside A exerts its anti-Aβ aggregation should be studied and elucidated in the future.
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Affiliation(s)
| | - Prasert Sobhon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Krai Meemon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
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Del Carmen SLM, Laura GV, Leonardo OL, Bernabé RRG, Antonio MRM. Aβ40 Oligomers Promote Survival and Early Neuronal Differentiation of Dentate Gyrus-Isolated Precursor Cells Through Activation of the Akt Signaling Pathway. Neurotox Res 2020; 38:611-625. [PMID: 32623694 DOI: 10.1007/s12640-020-00253-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 06/13/2020] [Accepted: 06/29/2020] [Indexed: 11/26/2022]
Abstract
The amyloid beta-peptide (Aβ) is the low-abundance product of amyloid precursor protein (APP), which is produced lifelong in the healthy brain. The functional properties of Aβ40 and Aβ42 peptides have not been completely elucidated to date. Although, several studies suggest that these peptides have a number of neurotrophic and neurotoxic properties, respectively. Interestingly, low concentrations of Aβ40 and Aβ42 regulate synaptic plasticity and improve cognitive functions, whereas the accumulation of Aβ42, coupled with the effects of age, can cause dysregulation of synaptic function, as is shown in Alzheimer's disease. Additionally, several studies suggest that both peptides, Aβ40 and Aβ42, are involved in neurogenic processes; however, these results are still controversial. Moreover, existing data indicate a direct relationship between the physicochemical characteristics of the peptides and their effects. Herein, we evaluated the effect of Aβ40 oligomers on hippocampal precursor cells isolated from the dentate gyrus of adult female C57Bl6 mice (mADGPCs). To this end, mADGPCs were treated with nanomolar and micromolar range concentrations of oligomeric forms of Aβ40 for 24, 48, and 72 h to evaluate their effects on several events in the neurogenic process in vitro, including viability, proliferation, and early differentiation. The results indicate that Aβ40 favors mADGPC proliferation, survival, and neuronal differentiation following a mechanism that involves activation of the Akt signaling pathway. Thus, this study provides evidence about the positive effects of Aβ40 oligomers on the neurogenic process in adult mouse hippocampal precursor cells in vitro.
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Affiliation(s)
- Silva-Lucero María Del Carmen
- Laboratory of Neurogenesis, Division of Clinical Investigations, National Institute of Psychiatry "Ramón de la Fuente Muñiz", Calzada México-Xochimilco 101, 14370, Mexico City, Mexico
- Department of Molecular Biomedicine, Center for Research and Advanced Studies (CINVESTAV-IPN), Av. Instituto Politécnico Nacional 2508, 07360, Mexico City, Mexico
| | - Gómez-Virgilio Laura
- Laboratory of Neurogenesis, Division of Clinical Investigations, National Institute of Psychiatry "Ramón de la Fuente Muñiz", Calzada México-Xochimilco 101, 14370, Mexico City, Mexico
- Department of Molecular Biomedicine, Center for Research and Advanced Studies (CINVESTAV-IPN), Av. Instituto Politécnico Nacional 2508, 07360, Mexico City, Mexico
| | - Ortíz-López Leonardo
- Laboratory of Neurogenesis, Division of Clinical Investigations, National Institute of Psychiatry "Ramón de la Fuente Muñiz", Calzada México-Xochimilco 101, 14370, Mexico City, Mexico
| | - Ramírez-Rodríguez Gerardo Bernabé
- Laboratory of Neurogenesis, Division of Clinical Investigations, National Institute of Psychiatry "Ramón de la Fuente Muñiz", Calzada México-Xochimilco 101, 14370, Mexico City, Mexico.
| | - Meraz-Ríos Marco Antonio
- Department of Molecular Biomedicine, Center for Research and Advanced Studies (CINVESTAV-IPN), Av. Instituto Politécnico Nacional 2508, 07360, Mexico City, Mexico.
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Raskatov JA. Conformational Selection as the Driving Force of Amyloid β Chiral Inactivation. Chembiochem 2020; 21:2945-2949. [PMID: 32424959 DOI: 10.1002/cbic.202000237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/17/2020] [Indexed: 12/19/2022]
Abstract
We recently introduced amyloid β chiral inactivation (Aβ-CI) as a molecular approach that uses mirror-image peptides to chaperone the natural Aβ stereoisomer into a less toxic state. The oligomer-to-fibril conversion mechanism remains the subject of active research. Perhaps the most striking feature of Aβ-CI is the virtual obliteration of the incubation/induction phase that is so characteristic of Aβ fibril formation kinetics. This qualitative change is indicative of the distinct mechanistic pathway Aβ-CI operates through. The current working model of Aβ-CI invokes the formation of "rippled" cross-β sheets, in which alternating l- and d-peptide strands form periodic networks. However, the assumption of rippled cross-β sheets does not per se explain the dramatic changes in reaction kinetics upon mixing of Aβ enantiomers. Herein, it is shown by DFT computational methods that the individual peptide strands in rippled cross-β networks are less conformationally strained than their pleated counterparts. This means that the adoption of fibril-seeding conformations is more probable for rippled cross-β. Conformational selection is thus suggested as the mechanistic rationale for the acceleration of fibril formation upon Aβ-CI.
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Affiliation(s)
- Jevgenij A Raskatov
- Department of Chemistry and Biochemistry, University of California Santa Cruz Physical Science Building 356, 1156 High Street, Santa Cruz, CA 95064, USA
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28
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Aggarwal L, Biswas P. Interaction Volume Is a Measure of the Aggregation Propensity of Amyloid-β. J Phys Chem Lett 2020; 11:3993-4000. [PMID: 32352786 DOI: 10.1021/acs.jpclett.0c00922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This study highlights the significance of the partial molar volume of amino acids in predicting the aggregation propensity of an intrinsically disordered protein, amyloid-β (Aβ), and its mutants in aqueous solution. The change in the interaction volume of the protein or mutant is quantitatively correlated with its calculated experimental aggregation propensity. This method also reveals how the interaction volume may be tuned by changing the charge and hydrophobicity of Aβ. While a positive change in the interaction volume and a higher aggregation propensity are observed for mutants with a decrease in the overall charge and/or an increase in hydrophobicity, a reverse trend is observed for the mutants with a decrease in the hydrophobicity and/or an increase in its charge. Hence, the interaction volume may be considered as a key parameter for monitoring protein aggregation that bridges the gap between the experimental aggregation kinetics and solvation thermodynamics.
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Affiliation(s)
- Leena Aggarwal
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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29
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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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30
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Aggarwal L, Biswas P. Effect of Alzheimer’s Disease Causative and Protective Mutations on the Hydration Environment of Amyloid-β. J Phys Chem B 2020; 124:2311-2322. [DOI: 10.1021/acs.jpcb.9b10425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Leena Aggarwal
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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31
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Fan Q, Liu Y, Wang X, Zhang Z, Fu Y, Liu L, Wang P, Ma H, Ma H, Seeram NP, Zheng J, Zhou F. Ginnalin A Inhibits Aggregation, Reverses Fibrillogenesis, and Alleviates Cytotoxicity of Amyloid β(1-42). ACS Chem Neurosci 2020; 11:638-647. [PMID: 31967782 DOI: 10.1021/acschemneuro.9b00673] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Aggregation of misfolded amyloid beta (Aβ) peptides into neurotoxic oligomers and fibrils has been implicated as a key event in the etiopathogenesis of Alzheimer's disease (AD). Ginnalin A (GA), a polyphenolic compound isolated from the red maple (Acer rubrum), has been found to possess anticancer, antiglycation, and antioxidation properties. Using thioflavin T (ThT) fluorescence, surface plasmon resonance (SPR), and atomic force microscopy (AFM), we demonstrate that GA can also effectively inhibit Aβ aggregation by primarily binding to Aβ monomers in a dose-dependent manner. Furthermore, GA can bind to multiple sites of Aβ aggregates to disassemble preformed fibrils and convert them into small aggregates. Circular dichroism (CD) spectra showed that these small aggregates are much less abundant in β-sheets, while cell viability assay confirms that they are essentially innocuous. Molecular dynamics (MD) simulations revealed that GA preferentially contacts with the C- and N-terminal β-sheets and the U-turn region of Aβ(1-42) oligomers through hydrophobic interactions and hydrogen bonding. Compared with other natural compounds that have shown promise in anti-Aβ fibrillogenesis and ameliorating Aβ-induced cytotoxicity, GA is unique in that it exhibits a more efficient inhibition of Aβ aggregation at the very early stage through its strong interaction with Aβ monomers and exerts its inhibitory effect at a lower dosage.
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Affiliation(s)
- Qi Fan
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, P. R. China
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, China
| | - Yonglan Liu
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Xiaoying Wang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Zhuang Zhang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Yaru Fu
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Luyao Liu
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Pengcheng Wang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Hongmin Ma
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, China
| | - Hang Ma
- Bioactive Botanical Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, The University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Navindra P. Seeram
- Bioactive Botanical Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, The University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Feimeng Zhou
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, P. R. China
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Liyanage SI, Weaver DF. Misfolded proteins as a therapeutic target in Alzheimer's disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 118:371-411. [PMID: 31928732 DOI: 10.1016/bs.apcsb.2019.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
For decades, Alzheimer's Disease (AD) was defined as a disorder of protein misfolding and aggregation. In particular, the extracellular peptide fragment: amyloid-β (Aβ), and the intracellular microtubule-associated protein: tau, were thought to initiate a neurodegenerative cascade which culminated in AD's progressive loss of memory and executive function. As such, both proteins became the focus of intense scrutiny, and served as the principal pathogenic target for hundreds of clinical trials. However, with varying efficacy, none of these investigations produced a disease-modifying therapy - offering patients with AD little recourse aside from transient, symptomatic medications. The near universal failure of clinical trials is unprecedented for a major research discipline. In part, this has motivated an increasing skepticism of the relevance of protein misfolding to AD's etiology. Several recent observations, principally the presence of significant protein pathologies in non-demented seniors, have lent credence to an apparent cursory role for Aβ and tau. Herein, we review both Aβ and tau, examining the processes from their biosynthesis to their pathogenesis and evaluate their vulnerability to medicinal intervention. We further attempt to reconcile the apparent failure of trials with the potential these targets hold. Ultimately, we seek to answer if protein misfolding is a viable platform in the pursuit of a disease-arresting strategy for AD.
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Affiliation(s)
- S Imindu Liyanage
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Donald F Weaver
- Krembil Research Institute, University Health Network, Toronto, ON, Canada; Departments of Medicine (Neurology), Chemistry and Pharmaceutical Sciences, University of Toronto, Toronto, ON, Canada
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33
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Xing X, Liu C, Yang H, Nouman MF, Ai H. Folding dynamics of Aβ42 monomer at pH 4.0–7.5 with and without physiological salt conditions – does the β1 or β2 region fold first? NEW J CHEM 2020. [DOI: 10.1039/d0nj01090a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The seeding region of Aβ42 monomer is jointly affected by the solution acidity, ionic distribution of the salt, and charged residues.
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Affiliation(s)
- Xiaofeng Xing
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- China
| | - Chengqiang Liu
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- China
| | - Huijuan Yang
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- China
| | | | - Hongqi Ai
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan
- China
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34
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Asadbegi M, Shamloo A. Identification of a Novel Multifunctional Ligand for Simultaneous Inhibition of Amyloid-Beta (Aβ 42) and Chelation of Zinc Metal Ion. ACS Chem Neurosci 2019; 10:4619-4632. [PMID: 31566950 DOI: 10.1021/acschemneuro.9b00468] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Zinc binding to β-amyloid structure could promote amyloid-β aggregation, as well as reactive oxygen species (ROS) production, as suggested in many experimental and theoretical studies. Therefore, the introduction of multifunctional drugs capable of chelating zinc metal ion and inhibiting Aβ aggregation is a promising strategy in the development of AD treatment. The present study has evaluated the efficacy of a new bifunctional peptide drug using molecular docking and molecular dynamics (MD) simulations. This drug comprises two different domains, an inhibitor domain, obtained from the C-terminal hydrophobic region of Aβ, and a Zn2+ chelating domain, derived from rapeseed meal, merge with a linker. The multifunctionality of the ligand was evaluated using a comprehensive set of MD simulations spanning up to 3.2 μs including Aβ relaxation, ligand-Zn2+ bilateral interaction, and, more importantly, ligand-Zn2+-Aβ42 trilateral interactions. Analysis of the results strongly indicated that the bifunctional ligand can chelate zinc metal ion and avoid Aβ aggregation simultaneously. The present study illustrated that the proposed ligand has considerable hydrophobic interactions and hydrogen bonding with monomeric Aβ in the presence of zinc metal ion. Therefore, in light of these considerable interactions and contacts, the α-helical structure of Aβ has been enhanced, while the β-sheet formation is prevented and the α-helix native structure is protected. Furthermore, the analysis of interactions between Aβ and ligand-zinc complex revealed that the zinc metal ion is coordinated to Met13, the ending residue of the ligand and merely one residue in Aβ. The results have proven the previous experimental and theoretical findings in the literature about Aβ interactions with zinc metal ion and also Aβ interactions with the first domain of the proposed ligand. Moreover, the current research has evaluated the chelation using MD simulation and linear interaction energy (LIE) methods, and the result has been satisfactorily verified with previous experimental and theoretical (DFT) studies.
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Affiliation(s)
- Mohsen Asadbegi
- Sharif University of Technology, School of Mechanical Engineering, Tehran 94305, Iran
| | - Amir Shamloo
- Sharif University of Technology, School of Mechanical Engineering, Tehran 94305, Iran
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35
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Man VH, He X, Ji B, Liu S, Xie XQ, Wang J. Molecular Mechanism and Kinetics of Amyloid-β 42 Aggregate Formation: A Simulation Study. ACS Chem Neurosci 2019; 10:4643-4658. [PMID: 31660732 DOI: 10.1021/acschemneuro.9b00473] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
As an important neuropathological hallmark of Alzheimer's disease (AD), the oligomerization of amyloid-β (Aβ) peptides has been intensively investigated in both theoretical and experimental studies. However, the oligomerization space in terms of the kinetics, molecular mechanism, and oligomer structures remains mysterious to us. An equation that can quantitatively describe the time it takes for Aβ oligomers to appear in the human brain at a given Aβ monomer concentration is extremely vital for us to understand the development and disease progression of AD. In this study, we utilized molecular dynamics (MD) simulations to investigate the oligomerization of Aβ42 peptides at five different monomer concentrations. We have elucidated the formation pathways of Aβ tetramers, characterized the oligomer structures, estimated the oligomerization time for Aβ dimers, trimers, and tetramers, and for the first-time derived equations that could quantitatively describe the relationship between the oligomerization time and the monomer concentration. Applying these equations, our prediction of oligomerization time agrees well with the experimental and clinical findings, in spite of the limitations of our oligomerization simulations. We have found that the Aβ oligomerization time depends on the monomer concentration by a power of -2.4. The newly established equations will enable us to quantitatively estimate the risk score of AD, which is a function of age. Moreover, we have identified the most dominant pathway of forming Aβ tetramers, probably the most important and toxic Aβ oligomer. Our results have shown that the structures of Aβ42 dimer, trimer, and tetramer, which are distinguishable from each other, depend on the monomer concentration at which the oligomers form. Representative oligomer structures, which can serve as potential drug targets, have been identified by clustering analysis. The MD sampling adequacy has been validated by the excellent agreement between the calculated and measured collisional cross section (CCS) parameters (the prediction errors are within 2%). In a conclusion, this study provides the kinetics and structure basis for developing inhibitors to decelerate the Aβ oligomerization process.
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Affiliation(s)
- Viet Hoang Man
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Beihong Ji
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Shuhan Liu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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36
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Jokar S, Khazaei S, Behnammanesh H, Shamloo A, Erfani M, Beiki D, Bavi O. Recent advances in the design and applications of amyloid-β peptide aggregation inhibitors for Alzheimer's disease therapy. Biophys Rev 2019; 11:10.1007/s12551-019-00606-2. [PMID: 31713720 DOI: 10.1007/s12551-019-00606-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 10/31/2019] [Indexed: 01/05/2023] Open
Abstract
Alzheimer's disease (AD) is an irreversible neurological disorder that progresses gradually and can cause severe cognitive and behavioral impairments. This disease is currently considered a social and economic incurable issue due to its complicated and multifactorial characteristics. Despite decades of extensive research, we still lack definitive AD diagnostic and effective therapeutic tools. Consequently, one of the most challenging subjects in modern medicine is the need for the development of new strategies for the treatment of AD. A large body of evidence indicates that amyloid-β (Aβ) peptide fibrillation plays a key role in the onset and progression of AD. Recent studies have reported that amyloid hypothesis-based treatments can be developed as a new approach to overcome the limitations and challenges associated with conventional AD therapeutics. In this review, we will provide a comprehensive view of the challenges in AD therapy and pathophysiology. We also discuss currently known compounds that can inhibit amyloid-β (Aβ) aggregation and their potential role in advancing current AD treatments. We have specifically focused on Aβ aggregation inhibitors including metal chelators, nanostructures, organic molecules, peptides (or peptide mimics), and antibodies. To date, these molecules have been the subject of numerous in vitro and in vivo assays as well as molecular dynamics simulations to explore their mechanism of action and the fundamental structural groups involved in Aβ aggregation. Ultimately, the aim of these studies (and current review) is to achieve a rational design for effective therapeutic agents for AD treatment and diagnostics.
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Affiliation(s)
- Safura Jokar
- Department of Nuclear Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, P.O. BOX: 14155-6559, Tehran, Iran
| | - Saeedeh Khazaei
- Department of Pharmaceutical Biomaterials , Faculty of Pharmacy, Tehran University of Medical Sciences, P.O. BOX: 14155-6559, Tehran, Iran
| | - Hossein Behnammanesh
- Department of Nuclear Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, P.O. BOX: 14155-6559, Tehran, Iran
| | - Amir Shamloo
- Department of Mechanical Engineering, Sharif University of Technology, P.O. Box: 11365-11155, Tehran, Iran
| | - Mostafa Erfani
- Radiation Application Research School, Nuclear Science and Technology Research Institute (NSTRI), P.O. Box: 14155-1339, Tehran, Iran
| | - Davood Beiki
- Research Center for Nuclear Medicine, Tehran University of Medical Sciences, P.O. BOX: 14155-6559, Tehran, Iran
| | - Omid Bavi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, P.O. Box: 71555-313, Shiraz, Iran.
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37
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Zhao J, Li K, Wan K, Sun T, Zheng N, Zhu F, Ma J, Jiao J, Li T, Ni J, Shi X, Wang H, Peng Q, Ai J, Xu W, Liu S. Organoplatinum‐Substituted Polyoxometalate Inhibits β‐amyloid Aggregation for Alzheimer's Therapy. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910521] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jing Zhao
- School of Life Science and TechnologyMOE Key Laboratory of Micro-systems and Micro-structures ManufacturingHarbin Institute of Technology Harbin 150080 China
| | - Kexin Li
- School of Pharmaceutical SciencesHarbin Medical University Harbin 150081 China
| | - Kaiwei Wan
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology Beijing 100190 China
| | - Tiedong Sun
- School of Life Science and TechnologyMOE Key Laboratory of Micro-systems and Micro-structures ManufacturingHarbin Institute of Technology Harbin 150080 China
| | - Nannan Zheng
- School of Life Science and TechnologyMOE Key Laboratory of Micro-systems and Micro-structures ManufacturingHarbin Institute of Technology Harbin 150080 China
| | - Fanjiao Zhu
- School of Life Science and TechnologyMOE Key Laboratory of Micro-systems and Micro-structures ManufacturingHarbin Institute of Technology Harbin 150080 China
| | - Jichao Ma
- School of Pharmaceutical SciencesHarbin Medical University Harbin 150081 China
| | - Jia Jiao
- School of Life Science and TechnologyMOE Key Laboratory of Micro-systems and Micro-structures ManufacturingHarbin Institute of Technology Harbin 150080 China
| | - Tianchan Li
- School of Life Science and TechnologyMOE Key Laboratory of Micro-systems and Micro-structures ManufacturingHarbin Institute of Technology Harbin 150080 China
| | - Jinyuan Ni
- School of Life Science and TechnologyMOE Key Laboratory of Micro-systems and Micro-structures ManufacturingHarbin Institute of Technology Harbin 150080 China
| | - Xinghua Shi
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology Beijing 100190 China
| | - Hui Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyLaboratory of Theoretical and Computational NanoscienceCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology Beijing 100190 China
| | - Qiang Peng
- Department of Urologythe Fourth Hospital of Harbin Medical University Harbin 150001 China
| | - Jing Ai
- School of Pharmaceutical SciencesHarbin Medical University Harbin 150081 China
| | - Wanhai Xu
- Department of Urologythe Fourth Hospital of Harbin Medical University Harbin 150001 China
| | - Shaoqin Liu
- School of Life Science and TechnologyMOE Key Laboratory of Micro-systems and Micro-structures ManufacturingHarbin Institute of Technology Harbin 150080 China
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38
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Zhao J, Li K, Wan K, Sun T, Zheng N, Zhu F, Ma J, Jiao J, Li T, Ni J, Shi X, Wang H, Peng Q, Ai J, Xu W, Liu S. Organoplatinum-Substituted Polyoxometalate Inhibits β-amyloid Aggregation for Alzheimer's Therapy. Angew Chem Int Ed Engl 2019; 58:18032-18039. [PMID: 31591753 DOI: 10.1002/anie.201910521] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Indexed: 12/16/2022]
Abstract
Aggregated β-amyloid (Aβ) is widely considered as a key factor in triggering progressive loss of neuronal function in Alzheimer's disease (AD), so targeting and inhibiting Aβ aggregation has been broadly recognized as an efficient therapeutic strategy for curing AD. Herein, we designed and prepared an organic platinum-substituted polyoxometalate, (Me4 N)3 [PW11 O40 (SiC3 H6 NH2 )2 PtCl2 ] (abbreviated as PtII -PW11 ) for inhibiting Aβ42 aggregation. The mechanism of inhibition on Aβ42 aggregation by PtII -PW11 was attributed to the multiple interactions of PtII -PW11 with Aβ42 including coordination interaction of Pt2+ in PtII -PW11 with amino group in Aβ42 , electrostatic attraction, hydrogen bonding and van der Waals force. In cell-based assay, PtII -PW11 displayed remarkable neuroprotective effect for Aβ42 aggregation-induced cytotoxicity, leading to increase of cell viability from 49 % to 67 % at a dosage of 8 μm. More importantly, the PtII -PW11 greatly reduced Aβ deposition and rescued memory loss in APP/PS1 transgenic AD model mice without noticeable cytotoxicity, demonstrating its potential as drugs for AD treatment.
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Affiliation(s)
- Jing Zhao
- School of Life Science and Technology, MOE Key Laboratory of Micro-systems and Micro-structures Manufacturing, Harbin Institute of Technology, Harbin, 150080, China
| | - Kexin Li
- School of Pharmaceutical Sciences, Harbin Medical University, Harbin, 150081, China
| | - Kaiwei Wan
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Tiedong Sun
- School of Life Science and Technology, MOE Key Laboratory of Micro-systems and Micro-structures Manufacturing, Harbin Institute of Technology, Harbin, 150080, China
| | - Nannan Zheng
- School of Life Science and Technology, MOE Key Laboratory of Micro-systems and Micro-structures Manufacturing, Harbin Institute of Technology, Harbin, 150080, China
| | - Fanjiao Zhu
- School of Life Science and Technology, MOE Key Laboratory of Micro-systems and Micro-structures Manufacturing, Harbin Institute of Technology, Harbin, 150080, China
| | - Jichao Ma
- School of Pharmaceutical Sciences, Harbin Medical University, Harbin, 150081, China
| | - Jia Jiao
- School of Life Science and Technology, MOE Key Laboratory of Micro-systems and Micro-structures Manufacturing, Harbin Institute of Technology, Harbin, 150080, China
| | - Tianchan Li
- School of Life Science and Technology, MOE Key Laboratory of Micro-systems and Micro-structures Manufacturing, Harbin Institute of Technology, Harbin, 150080, China
| | - Jinyuan Ni
- School of Life Science and Technology, MOE Key Laboratory of Micro-systems and Micro-structures Manufacturing, Harbin Institute of Technology, Harbin, 150080, China
| | - Xinghua Shi
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Hui Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Qiang Peng
- Department of Urology, the Fourth Hospital of Harbin Medical University, Harbin, 150001, China
| | - Jing Ai
- School of Pharmaceutical Sciences, Harbin Medical University, Harbin, 150081, China
| | - Wanhai Xu
- Department of Urology, the Fourth Hospital of Harbin Medical University, Harbin, 150001, China
| | - Shaoqin Liu
- School of Life Science and Technology, MOE Key Laboratory of Micro-systems and Micro-structures Manufacturing, Harbin Institute of Technology, Harbin, 150080, China
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39
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Ren B, Zhang Y, Zhang M, Liu Y, Zhang D, Gong X, Feng Z, Tang J, Chang Y, Zheng J. Fundamentals of cross-seeding of amyloid proteins: an introduction. J Mater Chem B 2019; 7:7267-7282. [PMID: 31647489 DOI: 10.1039/c9tb01871a] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Misfolded protein aggregates formed by the same (homologous) or different (heterologous/cross) sequences are the pathological hallmarks of many protein misfolding diseases (PMDs) including Alzheimer's disease (AD) and type 2 diabetes (T2D). Different from homologous-amyloid aggregation that is solely associated with a specific PMD, cross-amyloid aggregation (i.e. cross-seeding) of different amyloid proteins is more fundamentally and biologically important for understanding and untangling not only the pathological process of each PMD, but also a potential molecular cross-talk between different PMDs. However, the cross-amyloid aggregation is still a subject poorly explored and little is known about its sequence/structure-dependent aggregation mechanisms, as compared to the widely studied homo-amyloid aggregation. Here, we review the most recent and important findings of amyloid cross-seeding behaviors from in vitro, in vivo, and in silico studies. Some typical cross-seeding phenomena between Aβ/hIAPP, Aβ/tau, Aβ/α-synuclein, and tau/α-synuclein are selected and presented, and the underlying specific or general cross-seeding mechanisms are also discussed to better reveal their sequence-structure-property relationships. The potential use of the cross-seeding concept to design amyloid inhibitors is also proposed. Finally, we offer some personal perspectives on current major challenges and future research directions in this less-studied yet important field, and hopefully this work will stimulate more research to explore all possible fundamental and practical aspects of amyloid cross-seeding.
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Affiliation(s)
- Baiping Ren
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
| | - Yanxian Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
| | - Mingzhen Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
| | - Yonglan Liu
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
| | - Dong Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
| | - Xiong Gong
- Department of Polymer Engineering, The University of Akron, Ohio, USA
| | - Zhangqi Feng
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Jianxin Tang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
| | - Yung Chang
- Department of Chemical Engineering, R&D Center for Membrane Technology, Chung Yuan Christian University, Taoyuan, Taiwan
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA.
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40
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Hashemi M, Zhang Y, Lv Z, Lyubchenko YL. Spontaneous self-assembly of amyloid β (1-40) into dimers. NANOSCALE ADVANCES 2019; 1:3892-3899. [PMID: 36132110 PMCID: PMC9417245 DOI: 10.1039/c9na00380k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/16/2019] [Indexed: 05/17/2023]
Abstract
The self-assembly and fibrillation of amyloid β (Aβ) proteins is the neuropathological hallmark of Alzheimer's disease. However, the molecular mechanism of how disordered monomers assemble into aggregates remains largely unknown. In this work, we characterize the assembly of Aβ (1-40) monomers into dimers using long-time molecular dynamics simulations. Upon interaction, the monomers undergo conformational transitions, accompanied by change of the structure, leading to the formation of a stable dimer. The dimers are stabilized by interactions in the N-terminal region (residues 5-12), in the central hydrophobic region (residues 16-23), and in the C-terminal region (residues 30-40); with inter-peptide interactions focused around the N- and C-termini. The dimers do not contain long β-strands that are usually found in fibrils.
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Affiliation(s)
- Mohtadin Hashemi
- Department of Pharmaceutical Sciences, 986025 Nebraska Medical Center, University of Nebraska Medical Center Omaha NE 68198 USA
| | - Yuliang Zhang
- Department of Pharmaceutical Sciences, 986025 Nebraska Medical Center, University of Nebraska Medical Center Omaha NE 68198 USA
- Biology and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory Livermore CA 94550 USA
| | - Zhengjian Lv
- Department of Pharmaceutical Sciences, 986025 Nebraska Medical Center, University of Nebraska Medical Center Omaha NE 68198 USA
- Bruker Nano Surfaces Division 112 Robin Hill Road Goleta, Santa Barbara CA 93117 USA
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, 986025 Nebraska Medical Center, University of Nebraska Medical Center Omaha NE 68198 USA
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41
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Iscen A, Brue CR, Roberts KF, Kim J, Schatz GC, Meade TJ. Inhibition of Amyloid-β Aggregation by Cobalt(III) Schiff Base Complexes: A Computational and Experimental Approach. J Am Chem Soc 2019; 141:16685-16695. [DOI: 10.1021/jacs.9b06388] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Aysenur Iscen
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Christopher R. Brue
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Kaleigh F. Roberts
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Joy Kim
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - George C. Schatz
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Thomas J. Meade
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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42
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J S Loureiro R, Vila-Viçosa D, Machuqueiro M, Shakhnovich EI, F N Faísca P. The Early Phase of β2m Aggregation: An Integrative Computational Study Framed on the D76N Mutant and the ΔN6 Variant. Biomolecules 2019; 9:biom9080366. [PMID: 31416179 PMCID: PMC6722664 DOI: 10.3390/biom9080366] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 08/08/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022] Open
Abstract
Human β2-microglobulin (b2m) protein is classically associated with dialysis-related amyloidosis (DRA). Recently, the single point mutant D76N was identified as the causative agent of a hereditary systemic amyloidosis affecting visceral organs. To get insight into the early stage of the β2m aggregation mechanism, we used molecular simulations to perform an in depth comparative analysis of the dimerization phase of the D76N mutant and the ΔN6 variant, a cleaved form lacking the first six N-terminal residues, which is a major component of ex vivo amyloid plaques from DRA patients. We also provide first glimpses into the tetramerization phase of D76N at physiological pH. Results from extensive protein–protein docking simulations predict an essential role of the C- and N-terminal regions (both variants), as well as of the BC-loop (ΔN6 variant), DE-loop (both variants) and EF-loop (D76N mutant) in dimerization. The terminal regions are more relevant under acidic conditions while the BC-, DE- and EF-loops gain importance at physiological pH. Our results recapitulate experimental evidence according to which Tyr10 (A-strand), Phe30 and His31 (BC-loop), Trp60 and Phe62 (DE-loop) and Arg97 (C-terminus) act as dimerization hot-spots, and further predict the occurrence of novel residues with the ability to nucleate dimerization, namely Lys-75 (EF-loop) and Trp-95 (C-terminus). We propose that D76N tetramerization is mainly driven by the self-association of dimers via the N-terminus and DE-loop, and identify Arg3 (N-terminus), Tyr10, Phe56 (D-strand) and Trp60 as potential tetramerization hot-spots.
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Affiliation(s)
- Rui J S Loureiro
- BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- BioISI-Biosystems & Integrative Sciences Institute and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Miguel Machuqueiro
- BioISI-Biosystems & Integrative Sciences Institute and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Patrícia F N Faísca
- BioISI-Biosystems & Integrative Sciences Institute and Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
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43
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Krupa P, Quoc Huy PD, Li MS. Properties of monomeric Aβ42 probed by different sampling methods and force fields: Role of energy components. J Chem Phys 2019. [DOI: 10.1063/1.5093184] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Pawel Krupa
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Pham Dinh Quoc Huy
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
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44
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Foley AR, Raskatov JA. A DFT-Assisted Topological Analysis of Four Polymorphic, S-Shaped Aβ42 Fibril Structures. Chembiochem 2019; 20:1722-1724. [PMID: 30821034 PMCID: PMC6713286 DOI: 10.1002/cbic.201900036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Indexed: 12/12/2022]
Abstract
Amyloid β 42 (Aβ42) is an inherently disordered peptide, whose toxic actions are believed to play important roles in the etiology of Alzheimer's disease. Four fibril structures of the peptide that display broadly similar characteristics were recently published, but a systematic comparison of these structures is lacking. In this paper, a topological framework was created to enable such understanding and produced new insights into subtle structural elements that underlie the overall structural diversity. A DFT-based analysis illuminated some of the energetic differences that arise as a consequence.
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Affiliation(s)
- Alejandro R. Foley
- Department of Chemistry and Biochemistry, Physical Science Building 356, 1156 High Street, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jevgenij A. Raskatov
- Department of Chemistry and Biochemistry, Physical Science Building 356, 1156 High Street, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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45
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Yoon J, Kim Y, Park JW. Binary Structure of Amyloid Beta Oligomers Revealed by Dual Recognition Mapping. Anal Chem 2019; 91:8422-8428. [PMID: 31140786 DOI: 10.1021/acs.analchem.9b01316] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Amyloid beta (Aβ) oligomers are widely considered to be the causative agent of Alzheimer's disease (AD), a progressive neurodegenerative disorder. Determining the structure of oligomers is, therefore, important for understanding the disease and developing therapeutic agents; however, elucidating the structure has been proven difficult due to heterogeneity, noncrystallinity, and variability. Herein, we investigated homo- and hetero-oligomers of Aβ40 and Aβ42 using atomic force microscopy (AFM) and revealed characteristics of the molecular structure. By examining the surface of individual oligomers with sequential N- and C-terminus specific antibody-tethered tips, we simultaneously mapped the N- and C-terminus distributions and the elastic modulus. Interestingly, both the N- and C-termini of Aβ peptides were recognized on the oligomer surface, and the termini detected pixel regions exhibited a lower elastic modulus than silent pixel regions. These two types of regions were randomly distributed on the oligomer surface.
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Affiliation(s)
- Jihyun Yoon
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Youngkyu Kim
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Joon Won Park
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
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46
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Liu C, Zhao W, Xing X, Shi H, Kang B, Liu H, Li P, Ai H. An Original Monomer Sampling from a Ready‐Made Aβ
42
NMR Fibril Suggests a Turn‐β‐Strand Synergetic Seeding Mechanism. Chemphyschem 2019; 20:1649-1660. [DOI: 10.1002/cphc.201801137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Chengqiang Liu
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
| | - Wei Zhao
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
| | - Xiaofeng Xing
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
| | - Hu Shi
- School of Chemistry and Chemical EngineeringShanxi University Taiyuan 030006 China
| | - Baotao Kang
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
| | - Haiying Liu
- School of PhysicsUniversity of Jinan Jinan 250022 China
| | - Ping Li
- Key Laboratory of Life-Organic Analysis, School of Chemistry and Chemical EngineeringQufu Normal University Qufu 273165 China
| | - Hongqi Ai
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
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47
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Weiffert T, Meisl G, Flagmeier P, De S, Dunning CJR, Frohm B, Zetterberg H, Blennow K, Portelius E, Klenerman D, Dobson CM, Knowles TPJ, Linse S. Increased Secondary Nucleation Underlies Accelerated Aggregation of the Four-Residue N-Terminally Truncated Aβ42 Species Aβ5-42. ACS Chem Neurosci 2019; 10:2374-2384. [PMID: 30793584 DOI: 10.1021/acschemneuro.8b00676] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Aggregation of the amyloid-β (Aβ) peptide into plaques is believed to play a crucial role in Alzheimer's disease. Amyloid plaques consist of fibrils of full length Aβ peptides as well as N-terminally truncated species. β-Site amyloid precursor protein-cleaving enzyme (BACE1) cleaves amyloid precursor protein in the first step in Aβ peptide production and is an attractive therapeutic target to limit Aβ generation. Inhibition of BACE1, however, induces a unique pattern of Aβ peptides with increased levels of N-terminally truncated Aβ peptides starting at position 5 (Aβ5-X), indicating that these peptides are generated through a BACE1-independent pathway. Here we elucidate the aggregation mechanism of Aβ5-42 and its influence on full-length Aβ42. We find that, compared to Aβ42, Aβ5-42 is more aggregation prone and displays enhanced nucleation rates. Aβ5-42 oligomers cause nonspecific membrane disruption to similar extent as Aβ42 but appear at earlier time points in the aggregation reaction. Noteworthy, this implies similar toxicity of Aβ42 and Aβ5-42 and the toxic species are generated faster by Aβ5-42. The increased rate of secondary nucleation on the surface of existing fibrils originates from a higher affinity of Aβ5-42 monomers for fibrils, as compared to Aβ42: an effect that may be related to the reduced net charge of Aβ5-42. Moreover, Aβ5-42 and Aβ42 peptides coaggregate into heteromolecular fibrils and either species can elongate existing Aβ42 or Aβ5-42 fibrils but Aβ42 fibrils are more catalytic than Aβ5-42 fibrils. Our findings highlight the importance of the N-terminus for surface-catalyzed nucleation and thus the production of toxic oligomers.
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Affiliation(s)
- Tanja Weiffert
- Department of Biochemistry and Structural Biology, Lund University, P O box 124, 221 00 Lund, Sweden
| | - Georg Meisl
- Centre for Misfolding Disease, Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick Flagmeier
- Centre for Misfolding Disease, Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Suman De
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Christopher J. R. Dunning
- Department of Biochemistry and Structural Biology, Lund University, P O box 124, 221 00 Lund, Sweden
| | - Birgitta Frohm
- Department of Biochemistry and Structural Biology, Lund University, P O box 124, 221 00 Lund, Sweden
| | - Henrik Zetterberg
- Institute of Neuroscience
and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska
Academy at the University of Gothenburg, 431 80 Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, 431 80 Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, WC1N 3BG London, United Kingdom
- UK Dementia Research Institute, WC1E 6BT London, United Kingdom
| | - Kaj Blennow
- Institute of Neuroscience
and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska
Academy at the University of Gothenburg, 431 80 Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, 431 80 Mölndal, Sweden
| | - Erik Portelius
- Institute of Neuroscience
and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska
Academy at the University of Gothenburg, 431 80 Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, 431 80 Mölndal, Sweden
| | - David Klenerman
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Christopher M. Dobson
- Centre for Misfolding Disease, Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Tuomas P. J. Knowles
- Centre for Misfolding Disease, Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, P O box 124, 221 00 Lund, Sweden
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48
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Narang SS, Goyal D, Goyal B. Inhibition of Alzheimer’s amyloid-β42 peptide aggregation by a bi-functional bis-tryptoline triazole: key insights from molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:1598-1611. [DOI: 10.1080/07391102.2019.1614093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Simranjeet Singh Narang
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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49
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Molecular dynamics investigation of halogenated amyloidogenic peptides. J Mol Model 2019; 25:124. [PMID: 31020417 DOI: 10.1007/s00894-019-4012-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/29/2019] [Indexed: 12/18/2022]
Abstract
Besides their biomolecular relevance, amyloids, generated by the self-assembly of peptides and proteins, are highly organized structures useful for nanotechnology applications. The introduction of halogen atoms in these peptides, and thus the possible formation of halogen bonds, allows further possibilities to finely tune the amyloid nanostructure. In this work, we performed molecular dynamics simulations on different halogenated derivatives of the β-amyloid peptide core-sequence KLVFF, by using a modified AMBER force field in which the σ-hole located on the halogen atom is modeled with a positively charged extra particle. The analysis of equilibrated structures shows good agreement with crystallographic data and experimental results, in particular concerning the formation of halogen bonds and the stability of the supramolecular structures. The modified force field described here allows describing the atomistic details contributing to peptides aggregation, with particular focus on the role of halogen bonds. This framework can potentially help the design of novel halogenated peptides with desired aggregation propensity. Graphical abstract Molecular dynamics investigation of halogenated amyloidogenic peptides.
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50
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Ilie IM, Caflisch A. Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates. Chem Rev 2019; 119:6956-6993. [DOI: 10.1021/acs.chemrev.8b00731] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ioana M. Ilie
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
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