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Polańska O, Szulc N, Stottko R, Olek M, Nadwodna J, Gąsior-Głogowska M, Szefczyk M. Challenges in Peptide Solubilization - Amyloids Case Study. CHEM REC 2024:e202400053. [PMID: 39023378 DOI: 10.1002/tcr.202400053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/23/2024] [Indexed: 07/20/2024]
Abstract
Peptide science has been a rapidly growing research field because of the enormous potential application of these biocompatible and bioactive molecules. However, many factors limit the widespread use of peptides in medicine, and low solubility is among the most common problems that hamper drug development in the early stages of research. Solubility is a crucial, albeit poorly understood, feature that determines peptide behavior. Several different solubility predictors have been proposed, and many strategies and protocols have been reported to dissolve peptides, but none of them is a one-size-fits-all method for solubilization of even the same peptide. In this review, we look for the reasons behind the difficulties in dissolving peptides, analyze the factors influencing peptide aggregation, conduct a critical analysis of solubilization strategies and protocols available in the literature, and give some tips on how to deal with the so-called difficult sequences. We focus on amyloids, which are particularly difficult to dissolve and handle such as amyloid beta (Aβ), insulin, and phenol-soluble modulins (PSMs).
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Affiliation(s)
- Oliwia Polańska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Natalia Szulc
- Department of Physics and Biophysics, Wroclaw University of Environmental and Life Sciences, Norwida 25, 50-375, Wrocław, Poland
| | - Rafał Stottko
- Faculty of Chemistry, Wrocław University of Science and Technology, Gdanska 7/9, 50-344, Wrocław, Poland
| | - Mateusz Olek
- Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Traugutta 2, 41-800 Zabrze, Poland
| | - Julita Nadwodna
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marlena Gąsior-Głogowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
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2
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Wagner WJ, Gross ML. Using mass spectrometry-based methods to understand amyloid formation and inhibition of alpha-synuclein and amyloid beta. MASS SPECTROMETRY REVIEWS 2024; 43:782-825. [PMID: 36224716 PMCID: PMC10090239 DOI: 10.1002/mas.21814] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Amyloid fibrils, insoluble β-sheets structures that arise from protein misfolding, are associated with several neurodegenerative disorders. Many small molecules have been investigated to prevent amyloid fibrils from forming; however, there are currently no therapeutics to combat these diseases. Mass spectrometry (MS) is proving to be effective for studying the high order structure (HOS) of aggregating proteins and for determining structural changes accompanying protein-inhibitor interactions. When combined with native MS (nMS), gas-phase ion mobility, protein footprinting, and chemical cross-linking, MS can afford regional and sometimes amino acid spatial resolution of the aggregating protein. The spatial resolution is greater than typical low-resolution spectroscopic, calorimetric, and the traditional ThT fluorescence methods used in amyloid research today. High-resolution approaches can struggle when investigating protein aggregation, as the proteins exist as complex oligomeric mixtures of many sizes and several conformations or polymorphs. Thus, MS is positioned to complement both high- and low-resolution approaches to studying amyloid fibril formation and protein-inhibitor interactions. This review covers basics in MS paired with ion mobility, continuous hydrogen-deuterium exchange (continuous HDX), pulsed hydrogen-deuterium exchange (pulsed HDX), fast photochemical oxidation of proteins (FPOP) and other irreversible labeling methods, and chemical cross-linking. We then review the applications of these approaches to studying amyloid-prone proteins with a focus on amyloid beta and alpha-synuclein. Another focus is the determination of protein-inhibitor interactions. The expectation is that MS will bring new insights to amyloid formation and thereby play an important role to prevent their formation.
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Affiliation(s)
- Wesley J Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
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3
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Song C, Li H, Zhang T, Zheng C, Zhang Y. Synergetic effect of matrine on the catalytic scFv antibody HS72 in vitro and in mice with Alzheimer disease pathology. Neuropharmacology 2024; 242:109775. [PMID: 37913984 DOI: 10.1016/j.neuropharm.2023.109775] [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: 08/08/2023] [Revised: 10/15/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023]
Abstract
Single-chain variable fragment (scFv) HS72 is a catalytic antibody that specifically degrades amyloid β-protein 1-42 (Aβ42) aggregates in vitro or reduces the level or burden of Aβ42 deposits/plaques in the brains of mice with Alzheimer disease pathology. Its efficacy has been shown in protecting neural cells in vitro and improving the morphology of the cell population in the brain of mice with AD pathology (AD mice). Matrine (Mat) is a natural product capable of binding to Aβ42 or its aggregates and blocking their neurotoxicity at concentrations of at least 10 μM or greater. However, this study revealed a synergistic effect of Mat on the catalytic effect of HS72 at low concentrations (0.01-2.5 μM). This is evidenced by the fact that Mat synergistically enhances HS72's ability to degrade Aβ42 aggregates and protect neural cells (SH-SY5Y and HT22 cells, and brain cells of AD mice). The molecular docking models and characterization of Mat's action both indicated that the mechanism of Mat's synergistic impact on HS72 catalysis is to increase the turnover number (or molecular activity) of HS72 by enhancing the catalytic power of the HS72's catalytic groups and encouraging the release of the degradation products (Aβ fragments). The study's results suggest a natural synergy between Mat-like small molecules and the catalytic anti-oligomeric Aβ42 antibody HS72, enabling more effective reduction or removal of Aβ42 aggregates or plaques than the antibody alone. These findings provide novel insights into the effectiveness of anti-oligomeric Aβ42 antibodies in AD immunotherapy.
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Affiliation(s)
- Chuli Song
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - He Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Tianyu Zhang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Changxin Zheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Yingjiu Zhang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China.
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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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5
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Gutierrez-Merino C. Brain Hydrophobic Peptides Antagonists of Neurotoxic Amyloid β Peptide Monomers/Oligomers-Protein Interactions. Int J Mol Sci 2023; 24:13846. [PMID: 37762148 PMCID: PMC10531495 DOI: 10.3390/ijms241813846] [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: 08/04/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Amyloid β (Aβ) oligomers have been linked to Alzheimer's disease (AD) pathogenesis and are the main neurotoxic forms of Aβ. This review focuses on the following: (i) the Aβ(1-42):calmodulin interface as a model for the design of antagonist Aβ peptides and its limitations; (ii) proteolytic degradation as the major source of highly hydrophobic peptides in brain cells; and (iii) brain peptides that have been experimentally demonstrated to bind to Aβ monomers or oligomers, Aβ fibrils, or Aβ plaques. It is highlighted that the hydrophobic amino acid residues of the COOH-terminal segment of Aβ(1-42) play a key role in its interaction with intracellular protein partners linked to its neurotoxicity. The major source of highly hydrophobic endogenous peptides of 8-10 amino acids in neurons is the proteasome activity. Many canonical antigen peptides bound to the major histocompatibility complex class 1 are of this type. These highly hydrophobic peptides bind to Aβ and are likely to be efficient antagonists of the binding of Aβ monomers/oligomers concentrations in the nanomolar range with intracellular proteins. Also, their complexation with Aβ will protect them against endopeptidases, suggesting a putative chaperon-like physiological function for Aβ that has been overlooked until now. Remarkably, the hydrophobic amino acid residues of Aβ responsible for the binding of several neuropeptides partially overlap with those playing a key role in its interaction with intracellular protein partners that mediates its neurotoxicity. Therefore, these latter neuropeptides are also potential candidates to antagonize Aβ peptides binding to target proteins. In conclusion, the analysis performed in this review points out that hydrophobic endogenous brain neuropeptides could be valuable biomarkers to evaluate the risk of the onset of sporadic AD, as well as for the prognosis of AD.
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Affiliation(s)
- Carlos Gutierrez-Merino
- Instituto de Biomarcadores de Patologías Moleculares, Universidad de Extremadura, 06006 Badajoz, Spain
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6
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Jin Y, Downey MA, Singh A, Buratto SK, Bowers MT. Computationally Designed Small Molecules Disassemble Both Soluble Oligomers and Protofibrils of Amyloid β-Protein Responsible for Alzheimer's Disease. ACS Chem Neurosci 2023; 14:2717-2726. [PMID: 37442126 DOI: 10.1021/acschemneuro.3c00266] [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: 07/15/2023] Open
Abstract
Alzheimer's disease (AD) is one of the world's most pressing health crises. AD is an incurable disease affecting more than 6.5 million Americans, predominantly the elderly, and in its later stages, leads to memory loss, dementia, and death. Amyloid β (Aβ) protein aggregates have been one of the pathological hallmarks of AD since its initial characterization. The early stages of Aβ accumulation and aggregation involve the formation of oligomers, which are considered neurotoxic and play a key role in further aggregation into fibrils that eventually appear in the brain as amyloid plaques. We have recently shown by combining ion mobility mass spectrometry (IM-MS) and atomic force microscopy (AFM) that Aβ42 rapidly forms dodecamers (12-mers) as the terminal oligomeric state, and these dodecamers seed the early formation of Aβ42 protofibrils. The link between soluble oligomers and fibril formation is one of the essential aspects for understanding the root cause of the disease state and is critical to developing therapeutic interventions. Utilizing a joint pharmacophore space (JPS) method, potential drugs have been designed specifically for amyloid-related diseases. These small molecules were generated based on crucial chemical features necessary for target selectivity. In this paper, we utilize our combined IM-MS and AFM methods to investigate the impact of three second-generation JPS small-molecule inhibitors, AC0201, AC0202, and AC0203, on dodecamer as well as fibril formation in Aβ42. Our results indicate that AC0201 works well as an inhibitor and remodeler of both dodecamers and fibril formation, AC0203 behaves less efficiently, and AC0202 is ineffective.
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Affiliation(s)
- Yingying Jin
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Matthew A Downey
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Ambuj Singh
- Department of Computer Science, University of California, Santa Barbara, California 93106, United States
- Acelot, Inc., 3160 Porter Drive, Suite 200, Palo Alto, California 94304, United States
| | - Steven K Buratto
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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7
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Shahpasand-Kroner H, Siddique I, Malik R, Linares GR, Ivanova MI, Ichida J, Weil T, Münch J, Sanchez-Garcia E, Klärner FG, Schrader T, Bitan G. Molecular Tweezers: Supramolecular Hosts with Broad-Spectrum Biological Applications. Pharmacol Rev 2023; 75:263-308. [PMID: 36549866 PMCID: PMC9976797 DOI: 10.1124/pharmrev.122.000654] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 12/24/2022] Open
Abstract
Lysine-selective molecular tweezers (MTs) are supramolecular host molecules displaying a remarkably broad spectrum of biologic activities. MTs act as inhibitors of the self-assembly and toxicity of amyloidogenic proteins using a unique mechanism. They destroy viral membranes and inhibit infection by enveloped viruses, such as HIV-1 and SARS-CoV-2, by mechanisms unrelated to their action on protein self-assembly. They also disrupt biofilm of Gram-positive bacteria. The efficacy and safety of MTs have been demonstrated in vitro, in cell culture, and in vivo, suggesting that these versatile compounds are attractive therapeutic candidates for various diseases, infections, and injuries. A lead compound called CLR01 has been shown to inhibit the aggregation of various amyloidogenic proteins, facilitate their clearance in vivo, prevent infection by multiple viruses, display potent anti-biofilm activity, and have a high safety margin in animal models. The inhibitory effect of CLR01 against amyloidogenic proteins is highly specific to abnormal self-assembly of amyloidogenic proteins with no disruption of normal mammalian biologic processes at the doses needed for inhibition. Therapeutic effects of CLR01 have been demonstrated in animal models of proteinopathies, lysosomal-storage diseases, and spinal-cord injury. Here we review the activity and mechanisms of action of these intriguing compounds and discuss future research directions. SIGNIFICANCE STATEMENT: Molecular tweezers are supramolecular host molecules with broad biological applications, including inhibition of abnormal protein aggregation, facilitation of lysosomal clearance of toxic aggregates, disruption of viral membranes, and interference of biofilm formation by Gram-positive bacteria. This review discusses the molecular and cellular mechanisms of action of the molecular tweezers, including the discovery of distinct mechanisms acting in vitro and in vivo, and the application of these compounds in multiple preclinical disease models.
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Affiliation(s)
- Hedieh Shahpasand-Kroner
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Ibrar Siddique
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Ravinder Malik
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Gabriel R Linares
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Magdalena I Ivanova
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Justin Ichida
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Tatjana Weil
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Jan Münch
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Elsa Sanchez-Garcia
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Frank-Gerrit Klärner
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Thomas Schrader
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine (H.S.-K., I.S., R.M., G.B.), Brain Research Institute (G.B.), and Molecular Biology Institute (G.B.), University of California, Los Angeles, California; Department of Stem Cell Biology & Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California (G.R.L., J.I.); Department of Neurology, University of Michigan, Ann Arbor, Michigan (M.I.I.); Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany (T.W., J.M.); and Department of Computational Biochemistry (E.S.-G.) and Faculty of Chemistry (F-G.K., T.S.), University of Duisburg-Essen, Essen, Germany
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8
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Gao W, Li Y, Xu W, Mei J, Wang C, Sajjad A, Ai H. Inhibitory Mechanisms of Three Modified Small Molecules on the Misfolding of Cu
2+
‐Aβ42 Complex in Different pH Conditions: Insights from MD/QM Studies. ChemistrySelect 2022. [DOI: 10.1002/slct.202202217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wenqi Gao
- School of Chemistry and Chemical Engineering University of Jinan Jinan 250022 China
| | - Ye Li
- School of Chemistry and Chemical Engineering University of Jinan Jinan 250022 China
| | - Wen Xu
- School of Chemistry and Chemical Engineering University of Jinan Jinan 250022 China
| | - Jinfei Mei
- School of Chemistry and Chemical Engineering University of Jinan Jinan 250022 China
| | - Chuanbo Wang
- School of Chemistry and Chemical Engineering University of Jinan Jinan 250022 China
| | - Ahmad Sajjad
- School of Chemistry and Chemical Engineering University of Jinan Jinan 250022 China
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering University of Jinan Jinan 250022 China
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9
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Shobo A, Röntgen A, Hancock MA, Multhaup G. Biophysical characterization as a tool to predict amyloidogenic and toxic properties of amyloid-β42 peptides. FEBS Lett 2022; 596:1401-1411. [PMID: 35466397 DOI: 10.1002/1873-3468.14358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/02/2022] [Accepted: 04/19/2022] [Indexed: 11/06/2022]
Abstract
Amyloid-β42 (Aβ42) peptides are central to the amyloid pathology in Alzheimer's disease (AD). As biological mimetics, properties of synthetic Aβ peptides usually vary between vendors and batches, thus impacting the reproducibility of experimental studies. Here, we tested recombinantly expressed Aβ42 (Asp1 to Ala42) against synthetic Aβ42 from different suppliers using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), circular dichroism (CD) spectroscopy, thioflavin T aggregation, surface plasmon resonance and MTT cell viability assays. Overall, our recombinant Aβ42 provided a reproducible mimetic of desired properties. Across experimental approaches, the combined detection of Aβ42 dimers and random coil to β-sheet transition only correlated with aggregation-prone and cytotoxic peptides. Conclusively, combining MALDI-MS with CD appears to provide a rapid, reliable means to predict the "bioactivity" of Aβ42.
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Affiliation(s)
- Adeola Shobo
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
| | - Alexander Röntgen
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada.,Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Mark A Hancock
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada.,SPR-MS Facility, McGill University, Montreal, QC, Canada
| | - Gerhard Multhaup
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada.,Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
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10
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Matuszyk MM, Garwood CJ, Ferraiuolo L, Simpson JE, Staniforth RA, Wharton SB. Biological and methodological complexities of beta-amyloid peptide: Implications for Alzheimer's disease research. J Neurochem 2021; 160:434-453. [PMID: 34767256 DOI: 10.1111/jnc.15538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/29/2021] [Accepted: 11/09/2021] [Indexed: 01/01/2023]
Abstract
Although controversial, the amyloid cascade hypothesis remains central to the Alzheimer's disease (AD) field and posits amyloid-beta (Aβ) as the central factor initiating disease onset. In recent years, there has been an increase in emphasis on studying the role of low molecular weight aggregates, such as oligomers, which are suggested to be more neurotoxic than fibrillary Aβ. Other Aβ isoforms, such as truncated Aβ, have also been implicated in disease. However, developing a clear understanding of AD pathogenesis has been hampered by the complexity of Aβ biochemistry in vitro and in vivo. This review explores factors contributing to the lack of consistency in experimental approaches taken to model Aβ aggregation and toxicity and provides an overview of the different techniques available to analyse Aβ, such as electron and atomic force microscopy, nuclear magnetic resonance spectroscopy, dye-based assays, size exclusion chromatography, mass spectrometry and SDS-PAGE. The review also explores how different types of Aβ can influence Aβ aggregation and toxicity, leading to variation in experimental outcomes, further highlighting the need for standardisation in Aβ preparations and methods used in current research.
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Affiliation(s)
- Martyna M Matuszyk
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Claire J Garwood
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Laura Ferraiuolo
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Julie E Simpson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | | | - Stephen B Wharton
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
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11
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Effects of Aβ-derived peptide fragments on fibrillogenesis of Aβ. Sci Rep 2021; 11:19262. [PMID: 34584131 PMCID: PMC8479085 DOI: 10.1038/s41598-021-98644-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/13/2021] [Indexed: 11/08/2022] Open
Abstract
Amyloid β (Aβ) peptide aggregation plays a central role in Alzheimer's disease (AD) etiology. AD drug candidates have included small molecules or peptides directed towards inhibition of Aβ fibrillogenesis. Although some Aβ-derived peptide fragments suppress Aβ fibril growth, comprehensive analysis of inhibitory potencies of peptide fragments along the whole Aβ sequence has not been reported. The aim of this work is (a) to identify the region(s) of Aβ with highest propensities for aggregation and (b) to use those fragments to inhibit Aβ fibrillogenesis. Structural and aggregation properties of the parent Aβ1-42 peptide and seven overlapping peptide fragments have been studied, i.e. Aβ1-10 (P1), Aβ6-15 (P2), Aβ11-20 (P3), Aβ16-25 (P4), Aβ21-30 (P5), Aβ26-36 (P6), and Aβ31-42 (P7). Structural transitions of the peptides in aqueous buffer have been monitored by circular dichroism and Fourier transform infrared spectroscopy. Aggregation and fibrillogenesis were analyzed by light scattering and thioflavin-T fluorescence. The mode of peptide-peptide interactions was characterized by fluorescence resonance energy transfer. Three peptide fragments, P3, P6, and P7, exhibited exceptionally high propensity for β-sheet formation and aggregation. Remarkably, only P3 and P6 exerted strong inhibitory effect on the aggregation of Aβ1-42, whereas P7 and P2 displayed moderate inhibitory potency. It is proposed that P3 and P6 intercalate between Aβ1-42 molecules and thereby inhibit Aβ1-42 aggregation. These findings may facilitate therapeutic strategies of inhibition of Aβ fibrillogenesis by Aβ-derived peptides.
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12
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Wang K, Na L, Duan M. The Pathogenesis Mechanism, Structure Properties, Potential Drugs and Therapeutic Nanoparticles against the Small Oligomers of Amyloid-β. Curr Top Med Chem 2021; 21:151-167. [PMID: 32938351 DOI: 10.2174/1568026620666200916123000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/02/2020] [Accepted: 08/13/2020] [Indexed: 12/27/2022]
Abstract
Alzheimer's Disease (AD) is a devastating neurodegenerative disease that affects millions of people in the world. The abnormal aggregation of amyloid β protein (Aβ) is regarded as the key event in AD onset. Meanwhile, the Aβ oligomers are believed to be the most toxic species of Aβ. Recent studies show that the Aβ dimers, which are the smallest form of Aβ oligomers, also have the neurotoxicity in the absence of other oligomers in physiological conditions. In this review, we focus on the pathogenesis, structure and potential therapeutic molecules against small Aβ oligomers, as well as the nanoparticles (NPs) in the treatment of AD. In this review, we firstly focus on the pathogenic mechanism of Aβ oligomers, especially the Aβ dimers. The toxicity of Aβ dimer or oligomers, which attributes to the interactions with various receptors and the disruption of membrane or intracellular environments, were introduced. Then the structure properties of Aβ dimers and oligomers are summarized. Although some structural information such as the secondary structure content is characterized by experimental technologies, detailed structures are still absent. Following that, the small molecules targeting Aβ dimers or oligomers are collected; nevertheless, all of these ligands have failed to come into the market due to the rising controversy of the Aβ-related "amyloid cascade hypothesis". At last, the recent progress about the nanoparticles as the potential drugs or the drug delivery for the Aβ oligomers are present.
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Affiliation(s)
- Ke Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Liu Na
- School of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Mojie Duan
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
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13
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Wang W, Zhao G, Dong X, Sun Y. Unexpected Function of a Heptapeptide-Conjugated Zwitterionic Polymer that Coassembles into β-Amyloid Fibrils and Eliminates the Amyloid Cytotoxicity. ACS APPLIED MATERIALS & INTERFACES 2021; 13:18089-18099. [PMID: 33829756 DOI: 10.1021/acsami.1c01132] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fibrillogenesis of amyloid β-protein (Aβ) is pathologically associated with Alzheimer's disease (AD), so modulating Aβ aggregation is crucial for AD prevention and treatment. Herein, a zwitterionic polymer with short dimethyl side chains (pID) is synthesized and conjugated with a heptapeptide inhibitor (Ac-LVFFARK-NH2, LK7) to construct zwitterionic polymer-inhibitor conjugates for enhanced inhibition of Aβ aggregation. However, it is unexpectedly found that the LK7@pID conjugates remarkably promote Aβ fibrillization to form more fibrils than the free Aβ system but effectively eliminate Aβ-induced cytotoxicity. Such an unusual behavior of the LK7@pID conjugates is unraveled by extensive mechanistic studies. First, the hydrophobic environment within the assembled micelles of LK7@pID promotes the hydrophobic interaction between Aβ molecules and LK7@pID, which triggers Aβ aggregation at the very beginning, making fibrillization occur at an earlier stage. Second, in the aggregation process, the LK7@pID micelles disassemble by the intensive interactions with Aβ, and LK7@pID participates in the fibrillization by being embedded in the Aβ fibrils, leading to the formation of hybrid and heterogeneous fibrillar aggregates with a different structure than normal Aβ fibrils. This unique Trojan horse-like feature of LK7@pID conjugates has not been observed for any other inhibitors reported previously and may shed light on the design of new modulators against β-amyloid cytotoxicity.
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Affiliation(s)
- Wenjuan Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Guangfu Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
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14
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Cawood EE, Karamanos TK, Wilson AJ, Radford SE. Visualizing and trapping transient oligomers in amyloid assembly pathways. Biophys Chem 2021; 268:106505. [PMID: 33220582 PMCID: PMC8188297 DOI: 10.1016/j.bpc.2020.106505] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 12/31/2022]
Abstract
Oligomers which form during amyloid fibril assembly are considered to be key contributors towards amyloid disease. However, understanding how such intermediates form, their structure, and mechanisms of toxicity presents significant challenges due to their transient and heterogeneous nature. Here, we discuss two different strategies for addressing these challenges: use of (1) methods capable of detecting lowly-populated species within complex mixtures, such as NMR, single particle methods (including fluorescence and force spectroscopy), and mass spectrometry; and (2) chemical and biological tools to bias the amyloid energy landscape towards specific oligomeric states. While the former methods are well suited to following the kinetics of amyloid assembly and obtaining low-resolution structural information, the latter are capable of producing oligomer samples for high-resolution structural studies and inferring structure-toxicity relationships. Together, these different approaches should enable a clearer picture to be gained of the nature and role of oligomeric intermediates in amyloid formation and disease.
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Affiliation(s)
- Emma E Cawood
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK.
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15
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Kapadia A, Sharma KK, Maurya IK, Singh V, Khullar M, Jain R. Structural and mechanistic insights into the inhibition of amyloid-β aggregation by Aβ 39-42 fragment derived synthetic peptides. Eur J Med Chem 2020; 212:113126. [PMID: 33395622 DOI: 10.1016/j.ejmech.2020.113126] [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: 11/10/2020] [Revised: 12/10/2020] [Accepted: 12/21/2020] [Indexed: 10/22/2022]
Abstract
The inhibition of amyloid-β (Aβ) aggregation is a promising approach towards therapeutic intervention for Alzheimer's disease (AD). Thirty eight tetrapeptides based upon Aβ39-42C-terminus fragment of the parent Aβ peptide were synthesized. The sequential replacement/modification employing unnatural amino acids imparted scaffold diversity, augmented activity, enhanced blood brain barrier permeability and offered proteolytic stability to the synthetic peptides. Several peptides exhibited promising protection against Aβ aggregation-mediated-neurotoxicity in PC-12 cells at doses ranged between 10 μM and 0.1 μM, further confirmed by the thioflavin-T fluorescence assay. CD study illustrate that these peptides restrict the β-sheet formation, and the non-appearance of Aβ42 fibrillar structures in the electron microscopy confirm the inhibition of Aβ42 aggregation. HRMS and ANS fluorescence spectroscopic analysis provided additional mechanistic insights. Two selected lead peptides 5 and 16 depicted enhanced blood-brain penetration and stability against serum and proteolytic enzyme. Structural insights into ligand-Aβ interactions on the monomeric and proto-fibrillar units of Aβ were computationally studied. Promising inhibitory potential and short sequence of the lead peptides offers new avenues for the advancement of peptide-derived therapeutics for AD.
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Affiliation(s)
- Akshay Kapadia
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar, Punjab, 160 062, India
| | - Krishna K Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar, Punjab, 160 062, India
| | - Indresh Kumar Maurya
- Department of Microbial Biotechnology, Punjab University, Sector 25, Chandigarh, 160 014, India
| | - Varinder Singh
- Post Graduate Institute of Medical Education and Research, Sector 11, Chandigarh, 160 014, India
| | - Madhu Khullar
- Post Graduate Institute of Medical Education and Research, Sector 11, Chandigarh, 160 014, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar, Punjab, 160 062, India.
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16
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Mason AJ, Hurst I, Malik R, Siddique I, Solomonov I, Sagi I, Klärner FG, Schrader T, Bitan G. Different Inhibitors of Aβ42-Induced Toxicity Have Distinct Metal-Ion Dependency. ACS Chem Neurosci 2020; 11:2243-2255. [PMID: 32559370 DOI: 10.1021/acschemneuro.0c00192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Oligomers of amyloid β-protein (Aβ) are thought to be the proximal toxic agents initiating the neuropathologic process in Alzheimer's disease (AD). Therefore, targeting the self-assembly and oligomerization of Aβ has been an important strategy for designing AD therapeutics. In parallel, research into the metallobiology of AD has shown that Zn2+ can strongly modulate the aggregation of Aβ in vitro and both promote and inhibit the neurotoxicity of Aβ, depending on the experimental conditions. Thus, successful inhibitors of Aβ self-assembly may have to inhibit the toxicity not only of Aβ oligomers themselves but also of Aβ-Zn2+ complexes. However, there has been relatively little research investigating the effects of Aβ self-assembly and toxicity inhibitors in the presence of Zn2+. Our group has characterized previously a series of Aβ42 C-terminal fragments (CTFs), some of which have been shown to inhibit Aβ oligomerization and neurotoxicity. Here, we asked whether three CTFs shown to be potent inhibitors of Aβ42 toxicity maintained their activity in the presence of Zn2+. Biophysical analysis showed that the CTFs had different effects on oligomer, β-sheet, and fibril formation by Aβ42-Zn2+ complexes. However, cell viability experiments in differentiated PC-12 cells incubated with Aβ42-Zn2+ complexes in the absence or presence of these CTFs showed that the CTFs completely lost their inhibitory activity in the presence of Zn2+ even when applied at 10-fold excess relative to Aβ42. In light of these results, we tested another inhibitor, the molecular tweezer CLR01, which coincidentally had been shown to have a high affinity for Zn2+, suggesting that it could disrupt both Aβ42 oligomerization and Aβ42-Zn2+ complexation. Indeed, we found that CLR01 effectively inhibited the toxicity of Aβ42-Zn2+ complexes. Moreover, it did so at a lower concentration than needed for inhibiting the toxicity of Aβ42 alone. In agreement with these results, CLR01 inhibited β-sheet and fibril formation in Aβ42-Zn2+ complexes. Our data suggest that, for the development of efficient therapeutic agents, inhibitors of Aβ self-assembly and toxicity should be examined in the presence of relevant metal ions and that molecular tweezers may be particularly attractive candidates for therapy development.
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Affiliation(s)
- Ashley J. Mason
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Ian Hurst
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Ravinder Malik
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Ibrar Siddique
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Inna Solomonov
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Frank-Gerrit Klärner
- Institute of Organic Chemistry, University of Duisburg-Essen, Essen 45117, Germany
| | - Thomas Schrader
- Institute of Organic Chemistry, University of Duisburg-Essen, Essen 45117, Germany
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, United States
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17
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Tonali N, Dodero VI, Kaffy J, Hericks L, Ongeri S, Sewald N. Real-Time BODIPY-Binding Assay To Screen Inhibitors of the Early Oligomerization Process of Aβ1-42 Peptide. Chembiochem 2020; 21:1129-1135. [PMID: 31702868 PMCID: PMC7217026 DOI: 10.1002/cbic.201900652] [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: 10/28/2019] [Indexed: 01/03/2023]
Abstract
Misfolding and aggregation of amyloid β1–42 peptide (Aβ1–42) play a central role in the pathogenesis of Alzheimer's disease (AD). Targeting the highly cytotoxic oligomeric species formed during the early stages of the aggregation process represents a promising therapeutic strategy to reduce the toxicity associated with Aβ1–42. Currently, the thioflavin T (ThT) assay is the only established spectrofluorometric method to screen aggregation inhibitors. The success of the ThT assay is that it can detect Aβ1–42 aggregates with high β‐sheet content, such as protofibrils or fibrils, which appear in the late aggregation steps. Unfortunately, by using the ThT assay, the detection of inhibitors of early soluble oligomers that present a low β‐sheet character is challenging. Herein, a new, facile, and robust boron‐dipyrromethene (BODIPY) real‐time assay suitable for 96‐well plate format, which allows screening of compounds as selective inhibitors of the formation of Aβ1–42 oligomers, is reported. These inhibitors decrease the cellular toxicity of Aβ1–42, although they fail in the ThT assay. The findings have been confirmed and validated by structural analysis and cell viability assays under comparable experimental conditions. It is demonstrated that the BODIPY assay is a convenient method to screen and discover new candidate compounds that slow down or stop the pathological early oligomerization process and are active in the cellular assay. Therefore, it is a suitable complementary screening method of the current ThT assay.
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Affiliation(s)
- Nicolo Tonali
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, P. O. Box 100131, 33501, Bielefeld, Germany.,BioCIS, CNRS/Université Paris Sud, Université Paris Saclay, 5 rue Jean-Baptiste Clément, 92296, Châtenay-Malabry Cedex, France
| | - Veronica I Dodero
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, P. O. Box 100131, 33501, Bielefeld, Germany
| | - Julia Kaffy
- BioCIS, CNRS/Université Paris Sud, Université Paris Saclay, 5 rue Jean-Baptiste Clément, 92296, Châtenay-Malabry Cedex, France
| | - Loreen Hericks
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, P. O. Box 100131, 33501, Bielefeld, Germany
| | - Sandrine Ongeri
- BioCIS, CNRS/Université Paris Sud, Université Paris Saclay, 5 rue Jean-Baptiste Clément, 92296, Châtenay-Malabry Cedex, France
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, P. O. Box 100131, 33501, Bielefeld, Germany
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18
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Zhang Y, Ren B, Zhang D, Liu Y, Zhang M, Zhao C, Zheng J. Design principles and fundamental understanding of biosensors for amyloid-β detection. J Mater Chem B 2020; 8:6179-6196. [DOI: 10.1039/d0tb00344a] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aβ as biomarker in Alzheimer’s disease (AD) drives the significant research efforts for developing different biosensors with different sensing strategies, materials, and mechanisms for Aβ detection.
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Affiliation(s)
- Yanxian Zhang
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
| | - Baiping Ren
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
| | - Dong Zhang
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
| | - Yonglan Liu
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
| | - Mingzhen Zhang
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
| | - Chao Zhao
- Department of Chemical and Biomolecular Engineering
- The University of Alabama
- USA
| | - Jie Zheng
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
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19
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Kapadia A, Patel A, Sharma KK, Maurya IK, Singh V, Khullar M, Jain R. Effect of C-terminus amidation of Aβ39–42fragment derived peptides as potential inhibitors of Aβ aggregation. RSC Adv 2020; 10:27137-27151. [PMID: 35515767 PMCID: PMC9055537 DOI: 10.1039/d0ra04788k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/10/2020] [Indexed: 11/21/2022] Open
Abstract
The C-terminus fragment (Val-Val-Ile-Ala) of amyloid-β is reported to inhibit the aggregation of the parent peptide. In an attempt to investigate the effect of sequential amino-acid scan and C-terminus amidation on the biological profile of the lead sequence, a series of tetrapeptides were synthesized using MW-SPPS. Peptide D-Phe-Val-Ile-Ala-NH2 (12c) exhibited high protection against β-amyloid-mediated-neurotoxicity by inhibiting Aβ aggregation in the MTT cell viability and ThT-fluorescence assay. Circular dichroism studies illustrate the inability of Aβ42 to form β-sheet in the presence of 12c, further confirmed by the absence of Aβ42 fibrils in electron microscopy experiments. The peptide exhibits enhanced BBB permeation, no cytotoxicity along with prolonged proteolytic stability. In silico studies show that the peptide interacts with the key amino acids in Aβ, which potentiate its fibrillation, thereby arresting aggregation propensity. This structural class of designed scaffolds provides impetus towards the rational development of peptide-based-therapeutics for Alzheimer's disease (AD). Amidated C-terminal fragment, Aβ39–42 derived non-cytotoxic β-sheet breaker peptides exhibit excellent potency, enhanced bioavailability and improved proteolytic stability.![]()
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Affiliation(s)
- Akshay Kapadia
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research
- India
| | - Aesan Patel
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research
- India
| | - Krishna K. Sharma
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research
- India
| | | | - Varinder Singh
- Post Graduate Institute of Medical Education and Research
- Chandigarh
- India
| | - Madhu Khullar
- Post Graduate Institute of Medical Education and Research
- Chandigarh
- India
| | - Rahul Jain
- Department of Medicinal Chemistry
- National Institute of Pharmaceutical Education and Research
- India
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20
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Lazzaro S, Ogrinc N, Lamont L, Vecchio G, Pappalardo G, Heeren RMA. Ion mobility spectrometry combined with multivariate statistical analysis: revealing the effects of a drug candidate for Alzheimer's disease on Aβ1-40 peptide early assembly. Anal Bioanal Chem 2019; 411:6353-6363. [PMID: 31407050 PMCID: PMC6718366 DOI: 10.1007/s00216-019-02030-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 07/04/2019] [Accepted: 07/10/2019] [Indexed: 12/20/2022]
Abstract
Inhibition of the initial stages of amyloid-β peptide self-assembly is a key approach in drug development for Alzheimer's disease, in which soluble and highly neurotoxic low molecular weight oligomers are produced and aggregate in the brain over time. Here we report a high-throughput method based on ion mobility mass spectrometry and multivariate statistical analysis to rapidly select statistically significant early-stage species of amyloid-β1-40 whose formation is inhibited by a candidate theranostic agent. Using this method, we have confirmed the inhibition of a Zn-porphyrin-peptide conjugate in the early self-assembly of Aβ40 peptide. The MS/MS fragmentation patterns of the species detected in the samples containing the Zn-porphyrin-peptide conjugate suggested a porphyrin-catalyzed oxidation at Met-35(O) of Aβ40. We introduce ion mobility MS combined with multivariate statistics as a systematic approach to perform data analytics in drug discovery/amyloid research that aims at the evaluation of the inhibitory effect on the Aβ early assembly in vitro models at very low concentration levels of Aβ peptides.
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Affiliation(s)
- Serena Lazzaro
- Institute of Biostructures and Bioimaging (IBB), National Research Council, Via Paolo Gaifami N.18, 95126, Catania, Italy
| | - Nina Ogrinc
- The Maastricht Multimodal Molecular Imaging institute M4I- Division of Imaging Mass Spectrometry, Maastricht University, Minderbroedersberg 4-6, 6211 LK, Maastricht, The Netherlands
| | - Lieke Lamont
- The Maastricht Multimodal Molecular Imaging institute M4I- Division of Imaging Mass Spectrometry, Maastricht University, Minderbroedersberg 4-6, 6211 LK, Maastricht, The Netherlands
| | - Graziella Vecchio
- Department of Chemical Sciences, Catania University, Viale Andrea Doria, 6, 95125, Catania, Italy
| | - Giuseppe Pappalardo
- Institute of Biostructures and Bioimaging (IBB), National Research Council, Via Paolo Gaifami N.18, 95126, Catania, Italy
| | - Ron M A Heeren
- The Maastricht Multimodal Molecular Imaging institute M4I- Division of Imaging Mass Spectrometry, Maastricht University, Minderbroedersberg 4-6, 6211 LK, Maastricht, The Netherlands.
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21
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Zhao G, Qi F, Dong X, Zheng J, Sun Y. LVFFARK conjugation to poly (carboxybetaine methacrylate) remarkably enhances its inhibitory potency on amyloid β-protein fibrillogenesis. REACT FUNCT POLYM 2019. [DOI: 10.1016/j.reactfunctpolym.2019.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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22
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Ryan P, Patel B, Makwana V, Jadhav HR, Kiefel M, Davey A, Reekie TA, Rudrawar S, Kassiou M. Peptides, Peptidomimetics, and Carbohydrate-Peptide Conjugates as Amyloidogenic Aggregation Inhibitors for Alzheimer's Disease. ACS Chem Neurosci 2018; 9:1530-1551. [PMID: 29782794 DOI: 10.1021/acschemneuro.8b00185] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder accounting for 60-80% of dementia cases. For many years, AD causality was attributed to amyloid-β (Aβ) aggregated species. Recently, multiple therapies that target Aβ aggregation have failed in clinical trials, since Aβ aggregation is found in AD and healthy patients. Attention has therefore shifted toward the aggregation of the tau protein as a major driver of AD. Numerous inhibitors of tau-based pathology have recently been developed. Diagnosis of AD has shifted from measuring late stage senile plaques to early stage biomarkers, amyloid-β and tau monomers and oligomeric assemblies. Synthetic peptides and some derivative structures are being explored for use as theranostic tools as they possess the capacity both to bind the biomarkers and to inhibit their pathological self-assembly. Several studies have demonstrated that O-linked glycoside addition can significantly alter amyloid aggregation kinetics. Furthermore, natural O-glycosylation of amyloid-forming proteins, including amyloid precursor protein (APP), tau, and α-synuclein, promotes alternative nonamyloidogenic processing pathways. As such, glycopeptides and related peptidomimetics are being investigated within the AD field. Here we review advancements made in the last 5 years, as well as the arrival of sugar-based derivatives.
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Affiliation(s)
- Philip Ryan
- School of Pharmacy and Pharmacology, Griffith University, Gold Coast 4222, Australia
| | - Bhautikkumar Patel
- School of Pharmacy and Pharmacology, Griffith University, Gold Coast 4222, Australia
| | - Vivek Makwana
- School of Pharmacy and Pharmacology, Griffith University, Gold Coast 4222, Australia
| | - Hemant R. Jadhav
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani Campus, Pilani-333031, Rajasthan, India
| | - Milton Kiefel
- Institute for Glycomics, Griffith University, Gold Coast 4222, Australia
| | - Andrew Davey
- School of Pharmacy and Pharmacology, Griffith University, Gold Coast 4222, Australia
- Menzies Health Institute Queensland, Griffith University, Gold Coast 4222, Australia
- Quality Use of Medicines Network, Griffith University, Gold Coast 4222, Australia
| | | | - Santosh Rudrawar
- School of Pharmacy and Pharmacology, Griffith University, Gold Coast 4222, Australia
- Menzies Health Institute Queensland, Griffith University, Gold Coast 4222, Australia
- Quality Use of Medicines Network, Griffith University, Gold Coast 4222, Australia
- School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Michael Kassiou
- School of Chemistry, The University of Sydney, NSW 2006, Australia
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Zhang H, Dong X, Liu F, Zheng J, Sun Y. Ac-LVFFARK-NH 2 conjugation to β-cyclodextrin exhibits significantly enhanced performance on inhibiting amyloid β-protein fibrillogenesis and cytotoxicity. Biophys Chem 2018; 235:40-47. [DOI: 10.1016/j.bpc.2018.02.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/12/2018] [Accepted: 02/04/2018] [Indexed: 11/16/2022]
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24
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Eyers CE, Vonderach M, Ferries S, Jeacock K, Eyers PA. Understanding protein–drug interactions using ion mobility–mass spectrometry. Curr Opin Chem Biol 2018; 42:167-176. [DOI: 10.1016/j.cbpa.2017.12.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/08/2017] [Accepted: 12/22/2017] [Indexed: 01/23/2023]
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25
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Hayden EY, Hoi KK, Lopez J, Inayathullah M, Condron MM, Teplow DB. Identification of key regions and residues controlling Aβ folding and assembly. Sci Rep 2017; 7:12434. [PMID: 28974765 PMCID: PMC5626695 DOI: 10.1038/s41598-017-10845-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/15/2017] [Indexed: 12/11/2022] Open
Abstract
Amyloid β-protein (Aβ) assembly is hypothesized to be a seminal neuropathologic event in Alzheimer’s disease (AD). We used an unbiased D-amino acid substitution strategy to determine structure-assembly relationships of 76 different Aβ40 and Aβ42 peptides. We determined the effects of the substitutions on peptide oligomerization, secondary structure dynamics, fibril assembly dynamics, and fibril morphology. Our experiments revealed that the assembly of Aβ42 was more sensitive to chiral substitutions than was Aβ40 assembly. Substitutions at identical positions in the two peptides often, but not always, produced the same effects on assembly. Sites causing substantial effects in both Aβ40 and Aβ42 include His14, Gln15, Ala30, Ile31, Met35, and Val36. Sites whose effects were unique to Aβ40 include Lys16, Leu17, and Asn 27, whereas sites unique to Aβ42 include Phe20 and Ala21. These sites may be appropriate targets for therapeutic agents that inhibit or potentiate, respectively, these effects.
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Affiliation(s)
- Eric Y Hayden
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Kimberly K Hoi
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA.,Department of Pediatrics and Department of Neurology, UCSF, San Francisco, CA, 94158, USA
| | - Jasmine Lopez
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Mohammed Inayathullah
- Biomaterials and Advanced Drug Delivery Laboratory, School of Medicine, Stanford University, Palo Alto, CA, 94304, USA
| | - Margaret M Condron
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - David B Teplow
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA. .,Molecular Biology Institute and Brain Research Institute; UCLA, Los Angeles, CA, 90095, USA.
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Identification of the primary peptide contaminant that inhibits fibrillation and toxicity in synthetic amyloid-β42. PLoS One 2017; 12:e0182804. [PMID: 28792968 PMCID: PMC5549942 DOI: 10.1371/journal.pone.0182804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 07/25/2017] [Indexed: 12/14/2022] Open
Abstract
Understanding the pathophysiology of Alzheimer disease has relied upon the use of amyloid peptides from a variety of sources, but most predominantly synthetic peptides produced using t-butyloxycarbonyl (Boc) or 9-fluorenylmethoxycarbonyl (Fmoc) chemistry. These synthetic methods can lead to minor impurities which can have profound effects on the biological activity of amyloid peptides. Here we used a combination of cytotoxicity assays, fibrillation assays and high resolution mass spectrometry (MS) to identify impurities in synthetic amyloid preparations that inhibit both cytotoxicity and aggregation. We identify the Aβ42Δ39 species as the major peptide contaminant responsible for limiting both cytotoxicity and fibrillation of the amyloid peptide. In addition, we demonstrate that the presence of this minor impurity inhibits the formation of a stable Aβ42 dimer observable by MS in very pure peptide samples. These results highlight the critical importance of purity and provenance of amyloid peptides in Alzheimer’s research in particular, and biological research in general.
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Soper-Hopper MT, Eschweiler JD, Ruotolo BT. Ion Mobility-Mass Spectrometry Reveals a Dipeptide That Acts as a Molecular Chaperone for Amyloid β. ACS Chem Biol 2017; 12:1113-1120. [PMID: 28240851 DOI: 10.1021/acschembio.7b00045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Previously, we discovered and structurally characterized a complex between amyloid β 1-40 and the neuropeptide leucine enkephalin. This work identified leucine enkephalin as a potentially useful starting point for the discovery of peptide-related biotherapeutics for Alzheimer's disease. In order to better understand such complexes that are formed in vitro, we describe here the analysis of a series of site-directed amino acid substitution variants of both peptides, covering the leucine enkephalin sequence in its entirety and a large number of selected residues of amyloid β 1-40 (residues: D1, E3, F4, R5, H6, Y10, E11, H13, H14, Q15, K16, E22, K28, and V40). Ion mobility-mass spectrometry measurements and molecular dynamics simulations reveal that the hydrophobic C-terminus of leucine enkephalin (Phe-Leu, FL) is crucial for the formation of peptide complexes. As such, we explore here the interaction of the dipeptide FL with both wildtype and variant forms of amyloid β in order to structurally characterize the complexes formed. We find that FL binds preferentially to amyloid β oligomers and attaches to amyloid β within the region between its N-terminus and its hydrophobic core, most specifically at residues Y10 and Q15. We further show that FL is able to prevent fibril formation.
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Affiliation(s)
- Molly T. Soper-Hopper
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joseph D. Eschweiler
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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Brinet D, Gaie-Levrel F, Delatour V, Kaffy J, Ongeri S, Taverna M. In vitro monitoring of amyloid β-peptide oligomerization by Electrospray differential mobility analysis: An alternative tool to evaluate Alzheimer's disease drug candidates. Talanta 2017; 165:84-91. [DOI: 10.1016/j.talanta.2016.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 12/04/2016] [Accepted: 12/06/2016] [Indexed: 11/27/2022]
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Xiong N, Zhao Y, Dong X, Zheng J, Sun Y. Design of a Molecular Hybrid of Dual Peptide Inhibitors Coupled on AuNPs for Enhanced Inhibition of Amyloid β-Protein Aggregation and Cytotoxicity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1601666. [PMID: 28112856 DOI: 10.1002/smll.201601666] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 12/07/2016] [Indexed: 05/28/2023]
Abstract
Aggregation of amyloid-β protein (Aβ) is a pathological hallmark of Alzheimer's disease (AD), so the inhibition of Aβ aggregation is an important strategy for the prevention and treatment of AD. Herein, we proposed to design molecular hybrids of peptide inhibitors by combining two peptide inhibitors, VVIA and LPFFD, into single sequences and examined their effects on Aβ42 aggregation and cytotoxicity. The hybrid peptides exhibit increased but moderate inhibitory activity as compared to their two precursors. By conjugating the peptides onto gold nanoparticles (AuNPs), however, the inhibition activity of the corresponding peptide@AuNPs against Aβ42 aggregation and cytotoxicity is greatly improved. Among them, VVIACLPFFD (VCD10)@AuNP is the most effective, which increases cell viability from 48% to 82% at a dosage as low as 0.1 nmol L-1 (NPs) or 40 nmol L-1 (peptide). The superior capacity of VCD10@AuNPs is considered due to its branched dual-inhibitor sequence, and its special surface orientation and conformation. These structural features promote its synergetic interactions with Aβ on AuNP surface, leading to strong inhibitions of Aβ oligomerization and fibrillation and the cytotoxicity caused by the aggregation species. The findings suggest that potent inhibitors can be derived by hybridization of multiple peptide inhibitors with the hybrid products coupled onto nanoparticles.
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Affiliation(s)
- Neng Xiong
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yanjiao Zhao
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
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30
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Das P, Chacko AR, Belfort G. Alzheimer's Protective Cross-Interaction between Wild-Type and A2T Variants Alters Aβ 42 Dimer Structure. ACS Chem Neurosci 2017; 8:606-618. [PMID: 28292185 DOI: 10.1021/acschemneuro.6b00357] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Whole genome sequencing has recently revealed the protective effect of a single A2T mutation in heterozygous carriers against Alzheimer's disease (AD) and age-related cognitive decline. The impact of the protective cross-interaction between the wild-type (WT) and A2T variants on the dimer structure is therefore of high interest, as the Aβ dimers are the smallest known neurotoxic species. Toward this goal, extensive atomistic replica exchange molecular dynamics simulations of the solvated WT homo- and A2T hetero- Aβ1-42 dimers have been performed, resulting into a total of 51 μs of sampling for each system. Weakening of a set of transient, intrachain contacts formed between the central and C-terminal hydrophobic residues is observed in the heterodimeric system. The majority of the heterodimers with reduced interaction between central and C-terminal regions lack any significant secondary structure and display a weak interchain interface. Interestingly, the A2T N-terminus, particularly residue F4, is frequently engaged in tertiary and quaternary interactions with central and C-terminal hydrophobic residues in those distinct structures, leading to hydrophobic burial. This atypical involvement of the N-terminus within A2T heterodimer revealed in our simulations implies possible interference on Aβ42 aggregation and toxic oligomer formation, which is consistent with experiments. In conclusion, the present study provides detailed structural insights onto A2T Aβ42 heterodimer, which might provide molecular insights onto the AD protective effect of the A2T mutation in the heterozygous state.
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Affiliation(s)
- Payel Das
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Anita R. Chacko
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Georges Belfort
- Howard
P. Isermann Department of Chemical and Biological Engineering, and
Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180-3590, United States
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Han X, Park J, Wu W, Malagon A, Wang L, Vargas E, Wikramanayake A, Houk KN, Leblanc RM. A resorcinarene for inhibition of Aβ fibrillation. Chem Sci 2017; 8:2003-2009. [PMID: 28451317 PMCID: PMC5398272 DOI: 10.1039/c6sc04854d] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 11/17/2016] [Indexed: 12/24/2022] Open
Abstract
Amyloid-β peptides (Aβ) fibrillation is the hallmark of Alzheimer's disease (AD). However, it has been challenging to discover potent agents in order to inhibit Aβ fibrillation. Herein, we demonstrated the effect of resorcinarene on inhibiting Aβ fibrillation in vitro via experimental and computational methods. Aβ were incubated with different concentrations of resorcinarene so as to monitor the kinetics by using thioflavin T binding assay. The results, which were further confirmed by far-UV CD spectroscopy and atomic force microscopy, strongly indicated that the higher concentration of resorcinarene, the more effective the inhibition of Aβ fibrillation. A cytotoxicity study showed that when sea urchin embryos were exposed to the resorcinarene, the majority survived due to the resorcinarene low toxicity. In addition, when the resorcinarene was added, the formation of toxic Aβ 42 species was delayed. Computational studies of Aβ fibrillation, including docking simulations and MD simulations, illustrated that the interaction between inhibitor resorcinarene and Aβ is driven by the non-polar interactions. These studies display a novel strategy for the exploration of promising antiamyloiddogenic agents for AD treatments.
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Affiliation(s)
- Xu Han
- Department of Chemistry , Cox Science Center , University of Miami , Coral Gables , Florida 33146 , USA .
| | - Jiyong Park
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , USA .
| | - Wei Wu
- Department of Biology , Cox Science Center , University of Miami , Coral Gables , Florida 33146 , USA
| | - Andres Malagon
- Departamento de Quimica , Universidad de los Andes , Cr. 1 No. 18A 10 , Bogota 111711 , Colombia
| | - Lingyu Wang
- Department of Biology , Cox Science Center , University of Miami , Coral Gables , Florida 33146 , USA
| | - Edgar Vargas
- Departamento de Quimica , Universidad de los Andes , Cr. 1 No. 18A 10 , Bogota 111711 , Colombia
| | - Athula Wikramanayake
- Department of Biology , Cox Science Center , University of Miami , Coral Gables , Florida 33146 , USA
| | - K N Houk
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , USA .
| | - Roger M Leblanc
- Department of Chemistry , Cox Science Center , University of Miami , Coral Gables , Florida 33146 , USA .
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32
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Urbanc B. Flexible N‐Termini of Amyloid β‐Protein Oligomers: A Link between Structure and Activity? Isr J Chem 2017. [DOI: 10.1002/ijch.201600097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Brigita Urbanc
- Department of Physics Drexel University Philadelphia, PA 19104 USA
- Faculty of Mathematics and Physics Jadranska ulica 19 1000 Ljubljana Slovenia
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33
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Liu J, Yang B, Ke J, Li W, Suen WC. Antibody-Based Drugs and Approaches Against Amyloid-β Species for Alzheimer’s Disease Immunotherapy. Drugs Aging 2016; 33:685-697. [DOI: 10.1007/s40266-016-0406-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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34
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Li H, Rahimi F, Bitan G. Modulation of Amyloid β-Protein (Aβ) Assembly by Homologous C-Terminal Fragments as a Strategy for Inhibiting Aβ Toxicity. ACS Chem Neurosci 2016; 7:845-56. [PMID: 27322435 DOI: 10.1021/acschemneuro.6b00154] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Self-assembly of amyloid β-protein (Aβ) into neurotoxic oligomers and fibrillar aggregates is a key process thought to be the proximal event leading to development of Alzheimer's disease (AD). Therefore, numerous attempts have been made to develop reagents that disrupt this process and prevent the formation of the toxic oligomers and aggregates. An attractive strategy for developing such reagents is to use peptides derived from Aβ based on the assumption that such peptides would bind to full-length Aβ, interfere with binding of additional full-length molecules, and thereby prevent formation of the toxic species. Guided by this rationale, most of the studies in the last two decades have focused on preventing formation of the core cross-β structure of Aβ amyloid fibrils using β-sheet-breaker peptides derived from the central hydrophobic cluster of Aβ. Though this approach is effective in inhibiting fibril formation, it is generally inefficient in preventing Aβ oligomerization. An alternative approach is to use peptides derived from the C-terminus of Aβ, which mediates both oligomerization and fibrillogenesis. This approach has been explored by several groups, including our own, and led to the discovery of several lead peptides with moderate to high inhibitory activity. Interestingly, the mechanisms of these inhibitory effects have been found to be diverse, and only in a small percentage of cases involved interference with β-sheet formation. Here, we review the strategy of using C-terminal fragments of Aβ as modulators of Aβ assembly and discuss the relevant challenges, therapeutic potential, and mechanisms of action of such fragments.
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Affiliation(s)
- Huiyuan Li
- West Virginia University, Morgantown, West Virginia 26506, United States
| | - Farid Rahimi
- Biomedical
Science and Biochemistry, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Gal Bitan
- Department
of Neurology, David Geffen School of Medicine, Brain Research Institute,
and Molecular Biology Institute, University of California at Los Angeles, Neuroscience Research Building 1, Room 451 635 Charles E. Young Drive
South, Los Angeles, California 90095-7334, United States
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35
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de Almeida NEC, Do TD, Tro M, LaPointe NE, Feinstein SC, Shea JE, Bowers MT. Opposing Effects of Cucurbit[7]uril and 1,2,3,4,6-Penta-O-galloyl-β-d-glucopyranose on Amyloid β25-35 Assembly. ACS Chem Neurosci 2016; 7:218-26. [PMID: 26629788 PMCID: PMC4758880 DOI: 10.1021/acschemneuro.5b00280] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease characterized by extracellular deposits of amyloid β protein (Aβ) in the brain. The conversion of soluble monomers to amyloid Aβ fibrils is a complicated process and involves several transient oligomeric species, which are widely believed to be highly toxic and play a crucial role in the etiology of AD. The development of inhibitors to prevent formation of small and midsized oligomers is a promising strategy for AD treatment. In this work, we employ ion mobility spectrometry (IMS), transmission electron microscopy (TEM), and molecular dynamics (MD) simulations to elucidate the structural modulation promoted by two potential inhibitors of Aβ oligomerization, cucurbit[7]uril (CB[7]) and 1,2,3,4,6-penta-O-galloyl-β-d-glucopyranose (PGG), on early oligomer and fibril formation of the Aβ25-35 fragment. One and two CB[7] molecules bind to Aβ25-35 monomers and dimers, respectively, and suppress aggregation by remodeling early oligomer structures and inhibiting the formation of higher-order oligomers. On the other hand, nonselective binding was observed between PGG and Aβ25-35. The interactions between PGG and Aβ25-35, surprisingly, enhanced the formation of Aβ aggregates by promoting extended Aβ25-35 conformations in both homo- and hetero-oligomers. When both ligands were present, the inhibitory effect of CB[7] overrode the stimulatory effect of PGG on Aβ25-35 aggregation, suppressing the formation of large amyloid oligomers and eliminating the structural conversion from isotropic to β-rich topologies induced by PGG. Our results provide mechanistic insights into CB[7] and PGG action on Aβ oligomerization. They also demonstrate the power of the IMS technique to investigate mechanisms of multiple small-molecule agents on the amyloid formation process.
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Affiliation(s)
- Natália E. C. de Almeida
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Thanh D. Do
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael Tro
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Nichole E. LaPointe
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, United States
| | - Stuart C. Feinstein
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Corresponding author: Michael T. Bowers. Tel: +1-805-893-2673;
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Wong AG, Wu C, Hannaberry E, Watson MD, Shea JE, Raleigh DP. Analysis of the Amyloidogenic Potential of Pufferfish (Takifugu rubripes) Islet Amyloid Polypeptide Highlights the Limitations of Thioflavin-T Assays and the Difficulties in Defining Amyloidogenicity. Biochemistry 2016; 55:510-8. [PMID: 26694855 PMCID: PMC5502355 DOI: 10.1021/acs.biochem.5b01107] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Islet amyloid polypeptide (IAPP, amylin) forms pancreatic amyloid in type-2 diabetes, a process that contributes to the loss of β-cell mass in the disease. IAPP has been found in all higher organisms examined, but not all species form amyloid and the ability to do so correlates with the primary sequence. The amyloidogenic potential of fish IAPPs has not been examined, although fish have been proposed as a source for xenobiotic transplantation. The sequence of pufferfish IAPP (Takifugu rubripes) is known and is the most divergent from human IAPP of any reported IAPP sequence, differing at 11 positions including seven located within residues 20-29, a segment of the molecule that is important for controlling amyloidogenicity. Several of the substitutions found in pufferfish IAPP are nonconservative including Ser to Pro, Asn to Thr, Ala to Tyr, and Leu to Tyr replacements, and several of these have not been reported in mammalian IAPP sequences. Amyloid prediction programs give conflicting results for pufferfish IAPP. CD spectroscopy, FTIR, and transmission electron microscopy reveal that pufferfish IAPP forms amyloid and does so more rapidly than human IAPP in tris buffer at pH 7.4, but does so more slowly in phosphate buffered saline (PBS) at pH 7.4. Molecular dynamics simulations indicate that the pufferfish sequence is compatible with models of IAPP amyloid. The fish polypeptide does not significantly bind to thioflavin-T in tris and does so only weakly in PBS. The results highlight difficulties with thioflavin-T assays and the ambiguity in defining amyloidogenicity.
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Affiliation(s)
- Amy G. Wong
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
| | - Chun Wu
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106-9510
| | - Eleni Hannaberry
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
| | - Matthew D. Watson
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106-9510
| | - Daniel P. Raleigh
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
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37
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Khatua P, Jose JC, Sengupta N, Bandyopadhyay S. Conformational features of the Aβ42 peptide monomer and its interaction with the surrounding solvent. Phys Chem Chem Phys 2016; 18:30144-30159. [DOI: 10.1039/c6cp04925g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Heterogeneous conformational flexibility of the Aβ monomers has been found to be correlated with the corresponding non-uniform entropy gains.
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Affiliation(s)
- Prabir Khatua
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
| | - Jaya C. Jose
- Physical Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Neelanjana Sengupta
- Department of Biological Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur-741246
- India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
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38
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Khan JM, Khan MS, Ali MS, Al-Shabib NA, Khan RH. Cetyltrimethylammonium bromide (CTAB) promote amyloid fibril formation in carbohydrate binding protein (concanavalin A) at physiological pH. RSC Adv 2016. [DOI: 10.1039/c6ra03707k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Low concentration of CTAB provoked cross β-sheet formation whereas high concentrations of CTAB direct to alpha helix induction in Con A.
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Affiliation(s)
- Javed Masood Khan
- Department of Food Science and Nutrition
- Faculty of Food and Agricultural Sciences
- King Saud University
- 2460 Riyadh 11451
- Saudi Arabia
| | - Mohd Shahnawaz Khan
- Protein Research Chair
- Department of Biochemistry
- College of Science
- King Saud University
- Riyadh
| | - Mohd Sajid Ali
- Department of Chemistry
- King Saud University
- Riyadh 11451
- Saudi Arabia
| | - Nasser Abdulatif Al-Shabib
- Department of Food Science and Nutrition
- Faculty of Food and Agricultural Sciences
- King Saud University
- 2460 Riyadh 11451
- Saudi Arabia
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit
- Aligarh Muslim University
- Aligarh
- India
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39
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Roychaudhuri R, Zheng X, Lomakin A, Maiti P, Condron MM, Benedek GB, Bitan G, Bowers MT, Teplow DB. Role of Species-Specific Primary Structure Differences in Aβ42 Assembly and Neurotoxicity. ACS Chem Neurosci 2015; 6:1941-55. [PMID: 26421877 PMCID: PMC4844016 DOI: 10.1021/acschemneuro.5b00180] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A variety of species express the amyloid β-protein (Aβ (the term "Aβ" refers both to Aβ40 and Aβ42, whereas "Aβ40" and "Aβ42" refer to each isoform specifically). Those species expressing Aβ with primary structure identical to that expressed in humans have been found to develop amyloid deposits and Alzheimer's disease-like neuropathology. In contrast, the Aβ sequence in mice and rats contains three amino acid substitutions, Arg5Gly, His13Arg, and Tyr10Phe, which apparently prevent the development of AD-like neuropathology. Interestingly, the brush-tailed rat, Octodon degus, expresses Aβ containing only one of these substitutions, His13Arg, and does develop AD-like pathology. We investigate here the biophysical and biological properties of Aβ peptides from humans, mice (Mus musculus), and rats (Octodon degus). We find that each peptide displays statistical coil → β-sheet secondary structure transitions, transitory formation of hydrophobic surfaces, oligomerization, formation of annuli, protofibrils, and fibrils, and an inverse correlation between rate of aggregation and aggregate size (faster aggregation produced smaller aggregates). The rank order of assembly rate was mouse > rat > Aβ42. The rank order of neurotoxicity of assemblies formed by each peptide immediately after preparation was Aβ42 > mouse ≈ rat. These data do not support long-standing hypotheses that the primary factor controlling development of AD-like neuropathology in rodents is Aβ sequence. Instead, the data support a hypothesis that assembly quaternary structure and organismal responses to toxic peptide assemblies mediate neuropathogenetic effects. The implication of this hypothesis is that a valid understanding of disease causation within a given system (organism, tissue, etc.) requires the coevaluation of both biophysical and cell biological properties of that system.
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Affiliation(s)
- Robin Roychaudhuri
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Xueyun Zheng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Aleksey Lomakin
- Department of Physics and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Panchanan Maiti
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Margaret M. Condron
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - George B. Benedek
- Department of Physics and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA
- Molecular Biology Institute and Brain Research Institute, University of California, Los Angeles, California 90095
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - David B. Teplow
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA
- Molecular Biology Institute and Brain Research Institute, University of California, Los Angeles, California 90095
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40
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Malishev R, Nandi S, Kolusheva S, Levi-Kalisman Y, Klärner FG, Schrader T, Bitan G, Jelinek R. Toxicity inhibitors protect lipid membranes from disruption by Aβ42. ACS Chem Neurosci 2015; 6:1860-9. [PMID: 26317327 DOI: 10.1021/acschemneuro.5b00200] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although the precise molecular factors linking amyloid β-protein (Aβ) to Alzheimer's disease (AD) have not been deciphered, interaction of Aβ with cellular membranes has an important role in the disease. However, most therapeutic strategies targeting Aβ have focused on interfering with Aβ self-assembly rather than with its membrane interactions. Here, we studied the impact of three toxicity inhibitors on membrane interactions of Aβ42, the longer form of Aβ, which is associated most strongly with AD. The inhibitors included the four-residue C-terminal fragment Aβ(39-42), the polyphenol (-)-epigallocatechin-3-gallate (EGCG), and the lysine-specific molecular tweezer, CLR01, all of which previously were shown to disrupt different steps in Aβ42 self-assembly. Biophysical experiments revealed that incubation of Aβ42 with each of the three modulators affected membrane interactions in a distinct manner. Interestingly, EGCG and CLR01 were found to have significant interaction with membranes themselves. However, membrane bilayer disruption was reduced when the compounds were preincubated with Aβ42, suggesting that binding of the assembly modulators to the peptide attenuated their membrane interactions. Importantly, our study reveals that even though the three tested compounds affect Aβ42 assembly differently, membrane interactions were significantly inhibited upon incubation of each compound with Aβ42, suggesting that preventing the interaction of Aβ42 with the membrane contributes substantially to inhibition of its toxicity by each compound. The data suggest that interference with membrane interactions is an important factor for Aβ42 toxicity inhibitors and should be taken into account in potential therapeutic strategies, in addition to disruption or remodeling of amyloid assembly.
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Affiliation(s)
- Ravit Malishev
- Department
of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Sukhendu Nandi
- Department
of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Sofiya Kolusheva
- Ilse
Katz Institute for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Yael Levi-Kalisman
- Department
of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Frank-Gerrit Klärner
- Institute
of Organic Chemistry, University of Duisburg-Essen, Essen 45117, Germany
| | - Thomas Schrader
- Institute
of Organic Chemistry, University of Duisburg-Essen, Essen 45117, Germany
| | - Gal Bitan
- Department
of Neurology, David Geffen School of Medicine, Brain Research Institute,
and Molecular Biology Institute, University of California at Los Angeles, Los
Angeles, California 90095, United States
| | - Raz Jelinek
- Department
of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
- Ilse
Katz Institute for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
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41
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Zheng X, Liu D, Roychaudhuri R, Teplow DB, Bowers MT. Amyloid β-Protein Assembly: Differential Effects of the Protective A2T Mutation and Recessive A2V Familial Alzheimer's Disease Mutation. ACS Chem Neurosci 2015; 6:1732-40. [PMID: 26244608 DOI: 10.1021/acschemneuro.5b00171] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Oligomeric states of the amyloid β-protein (Aβ) appear to be causally related to Alzheimer's disease (AD). Recently, two familial mutations in the amyloid precursor protein gene have been described, both resulting in amino acid substitutions at Ala2 (A2) within Aβ. An A2V mutation causes autosomal recessive early onset AD. Interestingly, heterozygotes enjoy some protection against development of the disease. An A2T substitution protects against AD and age-related cognitive decline in non-AD patients. Here, we use ion mobility-mass spectrometry (IM-MS) to examine the effects of these mutations on Aβ assembly. These studies reveal different assembly pathways for early oligomer formation for each peptide. A2T Aβ42 formed dimers, tetramers, and hexamers, but dodecamer formation was inhibited. In contrast, no significant effects on Aβ40 assembly were observed. A2V Aβ42 also formed dimers, tetramers, and hexamers, but it did not form dodecamers. However, A2V Aβ42 formed trimers, unlike A2T or wild-type (wt) Aβ42. In addition, the A2V substitution caused Aβ40 to oligomerize similar to that of wt Aβ42, as evidenced by the formation of dimers, tetramers, hexamers, and dodecamers. In contrast, wt Aβ40 formed only dimers and tetramers. These results provide a basis for understanding how these two mutations lead to, or protect against, AD. They also suggest that the Aβ N-terminus, in addition to the oft discussed central hydrophobic cluster and C-terminus, can play a key role in controlling disease susceptibility.
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Affiliation(s)
- Xueyun Zheng
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Deyu Liu
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Robin Roychaudhuri
- Department of Neurology, David Geffen School
of Medicine, Molecular Biology Institute and Brain Research Institute, University of California Los Angeles, Los Angeles, California 90095, United States
| | - David B. Teplow
- Department of Neurology, David Geffen School
of Medicine, Molecular Biology Institute and Brain Research Institute, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Michael T. Bowers
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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42
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Zheng X, Wu C, Liu D, Li H, Bitan G, Shea JE, Bowers MT. Mechanism of C-Terminal Fragments of Amyloid β-Protein as Aβ Inhibitors: Do C-Terminal Interactions Play a Key Role in Their Inhibitory Activity? J Phys Chem B 2015; 120:1615-23. [PMID: 26439281 DOI: 10.1021/acs.jpcb.5b08177] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Targeting the early oligomerization of amyloid β protein (Aβ) is a promising therapeutic strategy for Alzheimer's disease (AD). Recently, certain C-terminal fragments (CTFs) derived from Aβ42 were shown to be potent inhibitors of Aβ-induced toxicity. The shortest peptide studied, Aβ(39-42), has been shown to modulate Aβ oligomerization and inhibit Aβ toxicity. Understanding the mechanism of these CTFs, especially Aβ(39-42), is of significance for future therapeutic development of AD and peptidomimetic-based drug development. Here we used ion mobility spectrometry-mass spectrometry to investigate the interactions between two modified Aβ(39-42) derivatives, VVIA-NH2 and Ac-VVIA, and full-length Aβ42. VVIA-NH2 was previously shown to inhibit Aβ toxicity, whereas Ac-VVIA did not. Our mass spectrometry analysis revealed that VVIA-NH2 binds directly to Aβ42 monomer and small oligomers while Ac-VVIA binds only to Aβ42 monomer. Ion mobility studies showed that VVIA-NH2 modulates Aβ42 oligomerization by not only inhibiting the dodecamer formation but also disaggregating preformed Aβ42 dodecamer. Ac-VVIA also inhibits and removes preformed Aβ42 dodecamer. However, the Aβ42 sample with the addition of Ac-VVIA clogged the nanospray tip easily, indicating that larger aggregates are formed in the solution in the presence of Ac-VVIA. Molecular dynamics simulations suggested that VVIA-NH2 binds specifically to the C-terminal region of Aβ42 while Ac-VVIA binds dispersedly to multiple regions of Aβ42. This work implies that C-terminal interactions and binding to Aβ oligomers are important for C-terminal fragment inhibitors.
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Affiliation(s)
- Xueyun Zheng
- Department of Chemistry and Biochemistry and ∥Department of Physics, University of California , Santa Barbara, California 93106, United States.,Department of Neurology, David Geffen School of Medicine, §Brain Research Institute, and Molecular Biology Institute, University of California at Los Angeles , Los Angeles, California 90095, United States
| | - Chun Wu
- Department of Chemistry and Biochemistry and ∥Department of Physics, University of California , Santa Barbara, California 93106, United States.,Department of Neurology, David Geffen School of Medicine, §Brain Research Institute, and Molecular Biology Institute, University of California at Los Angeles , Los Angeles, California 90095, United States
| | - Deyu Liu
- Department of Chemistry and Biochemistry and ∥Department of Physics, University of California , Santa Barbara, California 93106, United States.,Department of Neurology, David Geffen School of Medicine, §Brain Research Institute, and Molecular Biology Institute, University of California at Los Angeles , Los Angeles, California 90095, United States
| | - Huiyuan Li
- Department of Chemistry and Biochemistry and ∥Department of Physics, University of California , Santa Barbara, California 93106, United States.,Department of Neurology, David Geffen School of Medicine, §Brain Research Institute, and Molecular Biology Institute, University of California at Los Angeles , Los Angeles, California 90095, United States
| | - Gal Bitan
- Department of Chemistry and Biochemistry and ∥Department of Physics, University of California , Santa Barbara, California 93106, United States.,Department of Neurology, David Geffen School of Medicine, §Brain Research Institute, and Molecular Biology Institute, University of California at Los Angeles , Los Angeles, California 90095, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry and ∥Department of Physics, University of California , Santa Barbara, California 93106, United States.,Department of Neurology, David Geffen School of Medicine, §Brain Research Institute, and Molecular Biology Institute, University of California at Los Angeles , Los Angeles, California 90095, United States
| | - Michael T Bowers
- Department of Chemistry and Biochemistry and ∥Department of Physics, University of California , Santa Barbara, California 93106, United States.,Department of Neurology, David Geffen School of Medicine, §Brain Research Institute, and Molecular Biology Institute, University of California at Los Angeles , Los Angeles, California 90095, United States
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43
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Pujol-Pina R, Vilaprinyó-Pascual S, Mazzucato R, Arcella A, Vilaseca M, Orozco M, Carulla N. SDS-PAGE analysis of Aβ oligomers is disserving research into Alzheimer´s disease: appealing for ESI-IM-MS. Sci Rep 2015; 5:14809. [PMID: 26450154 PMCID: PMC4598734 DOI: 10.1038/srep14809] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 09/09/2015] [Indexed: 12/20/2022] Open
Abstract
The characterization of amyloid-beta peptide (Aβ) oligomer forms and structures is crucial to the advancement in the field of Alzheimer´s disease (AD). Here we report a critical evaluation of two methods used for this purpose, namely sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), extensively used in the field, and ion mobility coupled to electrospray ionization mass spectrometry (ESI-IM-MS), an emerging technique with great potential for oligomer characterization. To evaluate their performance, we first obtained pure cross-linked Aβ40 and Aβ42 oligomers of well-defined order. Analysis of these samples by SDS-PAGE revealed that SDS affects the oligomerization state of Aβ42 oligomers, thus providing flawed information on their order and distribution. In contrast, ESI-IM-MS provided accurate information, while also reported on the chemical nature and on the structure of the oligomers. Our findings have important implications as they challenge scientific paradigms in the AD field built upon SDS-PAGE characterization of Aβ oligomer samples.
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Affiliation(s)
- Rosa Pujol-Pina
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | | | - Roberta Mazzucato
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Annalisa Arcella
- Joint IRB-BSC Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Marta Vilaseca
- Mass Spectrometry Core Facility, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Modesto Orozco
- Joint IRB-BSC Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain.,Department of Biochemistry and Molecular Biology, University of Barcelona, Diagonal 647, Barcelona 08028, Spain
| | - Natàlia Carulla
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
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44
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Das P, Murray B, Belfort G. Alzheimer's protective A2T mutation changes the conformational landscape of the Aβ₁₋₄₂ monomer differently than does the A2V mutation. Biophys J 2015; 108:738-47. [PMID: 25650940 DOI: 10.1016/j.bpj.2014.12.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/01/2014] [Accepted: 12/04/2014] [Indexed: 12/20/2022] Open
Abstract
The aggregation of amyloid-β (Aβ) peptides plays a crucial role in the etiology of Alzheimer's disease (AD). Recently, it has been reported that an A2T mutation in Aβ can protect against AD. Interestingly, a nonpolar A2V mutation also has been found to offer protection against AD in the heterozygous state, although it causes early-onset AD in homozygous carriers. Since the conformational landscape of the Aβ monomer is known to directly contribute to the early-stage aggregation mechanism, it is important to characterize the effects of the A2T and A2V mutations on Aβ₁₋₄₂ monomer structure. Here, we have performed extensive atomistic replica-exchange molecular dynamics simulations of the solvated wild-type (WT), A2V, and A2T Aβ₁₋₄₂ monomers. Our simulations reveal that although all three variants remain as collapsed coils in solution, there exist significant structural differences among them at shorter timescales. A2V exhibits an enhanced double-hairpin population in comparison to the WT, similar to those reported in toxic WT Aβ₁₋₄₂ oligomers. Such double-hairpin formation is caused by hydrophobic clustering between the N-terminus and the central and C-terminal hydrophobic patches. In contrast, the A2T mutation causes the N-terminus to engage in unusual electrostatic interactions with distant residues, such as K16 and E22, resulting in a unique population comprising only the C-terminal hairpin. These findings imply that a single A2X (where X = V or T) mutation in the primarily disordered N-terminus of the Aβ₁₋₄₂ monomer can dramatically alter the β-hairpin population and switch the equilibrium toward alternative structures. The atomistically detailed, comparative view of the structural landscapes of A2V and A2T variant monomers obtained in this study can enhance our understanding of the mechanistic differences in their early-stage aggregation.
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Affiliation(s)
- Payel Das
- Soft Matter Theory and Simulations Group, Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York.
| | - Brian Murray
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Georges Belfort
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
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45
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Arndt JR, Kondalaji SG, Maurer MM, Parker A, Legleiter J, Valentine SJ. Huntingtin N-Terminal Monomeric and Multimeric Structures Destabilized by Covalent Modification of Heteroatomic Residues. Biochemistry 2015; 54:4285-96. [PMID: 26098795 DOI: 10.1021/acs.biochem.5b00478] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Early stage oligomer formation of the huntingtin protein may be driven by self-association of the 17-residue amphipathic α-helix at the protein's N-terminus (Nt17). Oligomeric structures have been implicated in neuronal toxicity and may represent important neurotoxic species in Huntington's disease. Therefore, a residue-specific structural characterization of Nt17 is crucial to understanding and potentially inhibiting oligomer formation. Native electrospray ion mobility spectrometry-mass spectrometry (IMS-MS) techniques and molecular dynamics simulations (MDS) have been applied to study coexisting monomer and multimer conformations of Nt17, independent of the remainder of huntingtin exon 1. MDS suggests gas-phase monomer ion structures comprise a helix-turn-coil configuration and a helix-extended-coil region. Elongated dimer species comprise partially helical monomers arranged in an antiparallel geometry. This stacked helical bundle may represent the earliest stages of Nt17-driven oligomer formation. Nt17 monomers and multimers have been further probed using diethylpyrocarbonate (DEPC). An N-terminal site (N-terminus of Threonine-3) and Lysine-6 are modified at higher DEPC concentrations, which led to the formation of an intermediate monomer structure. These modifications resulted in decreased extended monomer ion conformers, as well as a reduction in multimer formation. From the MDS experiments for the dimer ions, Lys6 residues in both monomer constituents interact with Ser16 and Glu12 residues on adjacent peptides; therefore, the decrease in multimer formation could result from disruption of these or similar interactions. This work provides a structurally selective model from which to study Nt17 self-association and provides critical insight toward Nt17 multimerization and, possibly, the early stages of huntingtin exon 1 aggregation.
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Affiliation(s)
- James R Arndt
- †C. Eugene Bennett Department of Chemistry, ‡WVNano Safe Initiative, and §The Center for Neuroscience, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Samaneh Ghassabi Kondalaji
- †C. Eugene Bennett Department of Chemistry, ‡WVNano Safe Initiative, and §The Center for Neuroscience, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Megan M Maurer
- †C. Eugene Bennett Department of Chemistry, ‡WVNano Safe Initiative, and §The Center for Neuroscience, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Arlo Parker
- †C. Eugene Bennett Department of Chemistry, ‡WVNano Safe Initiative, and §The Center for Neuroscience, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Justin Legleiter
- †C. Eugene Bennett Department of Chemistry, ‡WVNano Safe Initiative, and §The Center for Neuroscience, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Stephen J Valentine
- †C. Eugene Bennett Department of Chemistry, ‡WVNano Safe Initiative, and §The Center for Neuroscience, West Virginia University, Morgantown, West Virginia 26506, United States
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46
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Politis A, Borysik AJ. Assembling the pieces of macromolecular complexes: Hybrid structural biology approaches. Proteomics 2015; 15:2792-803. [DOI: 10.1002/pmic.201400507] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/26/2015] [Accepted: 02/24/2015] [Indexed: 01/14/2023]
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47
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Xiong N, Dong XY, Zheng J, Liu FF, Sun Y. Design of LVFFARK and LVFFARK-functionalized nanoparticles for inhibiting amyloid β-protein fibrillation and cytotoxicity. ACS APPLIED MATERIALS & INTERFACES 2015; 7:5650-5662. [PMID: 25700145 DOI: 10.1021/acsami.5b00915] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Aggregation of amyloid β-protein (Aβ) into amyloid oligomers and fibrils is pathologically linked to Alzheimer's disease (AD). Hence, the inhibition of Aβ aggregation is essential for the prevention and treatment of AD, but the development of potent agents capable of inhibiting Aβ fibrillogenesis has posed significant challenges. Herein, we designed Ac-LVFFARK-NH2 (LK7) by incorporating two positively charged residues, R and K, into the central hydrophobic fragment of Aβ17-21 (LVFFA) and examined its inhibitory effect on Aβ42 aggregation and cytotoxicity by extensive physical, biophysical, and biological analyses. LK7 was observed to inhibit Aβ42 fibrillogenesis in a dose-dependent manner, but its strong self-assembly characteristic also resulted in high cytotoxicity. In order to prevent the cytotoxicity that resulted from the self-assembly of LK7, the peptide was then conjugated to the surface of poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) to fabricate a nanosized inhibitor, LK7@PLGA-NPs. It was found that LK7@PLGA-NPs had little cytotoxicity because the self-assembly of the LK7 conjugated on the NPs was completely inhibited. Moreover, the NPs-based inhibitor showed remarkable inhibitory capability against Aβ42 aggregation and significantly alleviated its cytotoxicity at a low LK7@PLGA-NPs concentration of 20 μg/mL. At the same peptide concentration, free LK7 showed little inhibitory effect. It is considered that several synergetic effects contributed to the strong inhibitory ability of LK7@PLGA-NPs, including the enhanced interactions between Aβ42 and LK7@PLGA-NPs brought on by inhibiting LK7 self-assembly, restricting conformational changes of Aβ42, and thus redirecting Aβ42 aggregation into unstructured, off-pathway aggregates. The working mechanisms of the inhibitory effects of LK7 and LK7@PLGA-NPs on Aβ42 aggregation were proposed based on experimental observations. This work provides new insights into the design and development of potent NPs-based inhibitors against Aβ aggregation and cytotoxicity.
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Affiliation(s)
- Neng Xiong
- †Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Xiao-Yan Dong
- †Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jie Zheng
- ‡Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Fu-Feng Liu
- †Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yan Sun
- †Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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48
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Zheng X, Liu D, Klärner FG, Schrader T, Bitan G, Bowers MT. Amyloid β-protein assembly: The effect of molecular tweezers CLR01 and CLR03. J Phys Chem B 2015; 119:4831-41. [PMID: 25751170 PMCID: PMC4415044 DOI: 10.1021/acs.jpcb.5b00692] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
![]()
The early oligomerization of amyloid
β-protein (Aβ)
has been shown to be an important event in the pathology of Alzheimer’s
disease (AD). Designing small molecule inhibitors targeting Aβ
oligomerization is one attractive and promising strategy for AD treatment.
Here we used ion mobility spectrometry coupled to mass spectrometry
(IMS-MS) to study the different effects of the molecular tweezers
CLR01 and CLR03 on Aβ self-assembly. CLR01 was found to bind
to Aβ directly and disrupt its early oligomerization. Moreover,
CLR01 remodeled the early oligomerization of Aβ42 by compacting
the structures of dimers and tetramers and as a consequence eliminated
higher-order oligomers. Unexpectedly, the negative-control derivative,
CLR03, which lacks the hydrophobic arms of the tweezer structure,
was found to facilitate early Aβ oligomerization. Our study
provides an example of IMS as a powerful tool to study and better
understand the interaction between small molecule modulators and Aβ
oligomerization, which is not attainable by other methods, and provides
important insights into therapeutic development of molecular tweezers
for AD treatment.
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Affiliation(s)
- Xueyun Zheng
- †Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Deyu Liu
- †Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Frank-Gerrit Klärner
- ‡Institute of Organic Chemistry, University of Duisburg-Essen, Essen 45117, Germany
| | - Thomas Schrader
- ‡Institute of Organic Chemistry, University of Duisburg-Essen, Essen 45117, Germany
| | - Gal Bitan
- §Department of Neurology, David Geffen School of Medicine, Brain Research Institute, and Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Michael T Bowers
- †Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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49
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Phillips AS, Gomes AF, Kalapothakis JMD, Gillam JE, Gasparavicius J, Gozzo FC, Kunath T, MacPhee C, Barran PE. Conformational dynamics of α-synuclein: insights from mass spectrometry. Analyst 2015; 140:3070-81. [DOI: 10.1039/c4an02306d] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Different mass spectrometry approaches are combined to investigate the conformational flexibility of α-synuclein.
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Affiliation(s)
- Ashley S. Phillips
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Alexandre F. Gomes
- Dalton Mass Spectrometry Laboratory
- University of Campinas – UNICAMP
- Brazil
| | | | - Jay E. Gillam
- School of Physics and Astronomy
- University of Edinburgh
- Edinburgh
- UK
| | | | - Fabio C. Gozzo
- Dalton Mass Spectrometry Laboratory
- University of Campinas – UNICAMP
- Brazil
| | - Tilo Kunath
- MRC Centre for Regenerative Medicine
- University of Edinburgh
- Edinburgh
- UK
| | - Cait MacPhee
- School of Physics and Astronomy
- University of Edinburgh
- Edinburgh
- UK
| | - Perdita E. Barran
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
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Jang H, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs. Chem Soc Rev 2014; 43:6750-64. [PMID: 24566672 PMCID: PMC4143503 DOI: 10.1039/c3cs60459d] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Aggregation of disordered amyloidogenic peptides into oligomers is the causative agent of amyloid-related diseases. In solution, disordered protein states are characterized by heterogeneous ensembles. Among these, β-rich conformers self-assemble via a conformational selection mechanism to form energetically-favored cross-β structures, regardless of their precise sequences. These disordered peptides can also penetrate the membrane, and electrophysiological data indicate that they form ion-conducting channels. Based on these and additional data, including imaging and molecular dynamics simulations of a range of amyloid peptides, Alzheimer's amyloid-β (Aβ) peptide, its disease-related variants with point mutations and N-terminal truncated species, other amyloidogenic peptides, as well as a cytolytic peptide and a synthetic gel-forming peptide, we suggest that disordered amyloidogenic peptides can also present a common motif in the membrane. The motif consists of curved, moon-like β-rich oligomers associated into annular organizations. The motif is favored in the lipid bilayer since it permits hydrophobic side chains to face and interact with the membrane and the charged/polar residues to face the solvated channel pores. Such channels are toxic since their pores allow uncontrolled leakage of ions into/out of the cell, destabilizing cellular ionic homeostasis. Here we detail Aβ, whose aggregation is associated with Alzheimer's disease (AD) and for which there are the most abundant data. AD is a protein misfolding disease characterized by a build-up of Aβ peptide as senile plaques, neurodegeneration, and memory loss. Excessively produced Aβ peptides may directly induce cellular toxicity, even without the involvement of membrane receptors through Aβ peptide-plasma membrane interactions.
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Affiliation(s)
- Hyunbum Jang
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, U.S.A
| | - Fernando Teran Arce
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Srinivasan Ramachandran
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Bruce L. Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California 90024, U.S.A
| | - Ratnesh Lal
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Ruth Nussinov
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, U.S.A
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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