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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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2
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Tsekrekou M, Giannakou M, Papanikolopoulou K, Skretas G. Protein aggregation and therapeutic strategies in SOD1- and TDP-43- linked ALS. Front Mol Biosci 2024; 11:1383453. [PMID: 38855322 PMCID: PMC11157337 DOI: 10.3389/fmolb.2024.1383453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/02/2024] [Indexed: 06/11/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with severe socio-economic impact. A hallmark of ALS pathology is the presence of aberrant cytoplasmic inclusions composed of misfolded and aggregated proteins, including both wild-type and mutant forms. This review highlights the critical role of misfolded protein species in ALS pathogenesis, particularly focusing on Cu/Zn superoxide dismutase (SOD1) and TAR DNA-binding protein 43 (TDP-43), and emphasizes the urgent need for innovative therapeutic strategies targeting these misfolded proteins directly. Despite significant advancements in understanding ALS mechanisms, the disease remains incurable, with current treatments offering limited clinical benefits. Through a comprehensive analysis, the review focuses on the direct modulation of the misfolded proteins and presents recent discoveries in small molecules and peptides that inhibit SOD1 and TDP-43 aggregation, underscoring their potential as effective treatments to modify disease progression and improve clinical outcomes.
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Affiliation(s)
- Maria Tsekrekou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Maria Giannakou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Katerina Papanikolopoulou
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
- ResQ Biotech, Patras Science Park, Rio, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- ResQ Biotech, Patras Science Park, Rio, Greece
- Institute for Bio-innovation, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
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3
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Liu X, Duan S, Jin Y, Walker E, Tsao M, Jang JH, Chen Z, Singh AK, Cantrell KL, Ingolfsson HI, Buratto SK, Bowers MT. Computationally Designed Molecules Modulate ALS-Related Amyloidogenic TDP-43 307-319 Aggregation. ACS Chem Neurosci 2023; 14:4395-4408. [PMID: 38050862 DOI: 10.1021/acschemneuro.3c00582] [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: 12/07/2023] Open
Abstract
Abnormal cytosolic aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) is observed in multiple diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration, and Alzheimer's disease. Previous studies have shown that TDP-43307-319 located at the C-terminal of TDP-43 can form higher-order oligomers and fibrils. Of particular interest are the hexamers that adopt a cylindrin structure that has been strongly correlated to neurotoxicity. In this study, we use the joint pharmacophore space (JPS) model to identify and generate potential TDP-43 inhibitors. Five JPS-designed molecules are evaluated using both experimental and computational methods: ion mobility mass spectrometry, thioflavin T fluorescence assay, circular dichroism spectroscopy, atomic force microscopy, and molecular dynamics simulations. We found that all five molecules can prevent the amyloid fibril formation of TDP-43307-319, but their efficacy varies significantly. Furthermore, among the five molecules, [AC0101] is the most efficient in preventing the formation of higher-order oligomers and dissociating preformed higher-order oligomers. Molecular dynamics simulations show that [AC0101] both is the most flexible and forms the most hydrogen bonds with the TDP-43307-319 monomer. The JPS-designed molecules can insert themselves between the β-strands in the hexameric cylindrin structure of TDP-43307-319 and can open its structure. Possible mechanisms for JPS-designed molecules to inhibit and dissociate TDP-43307-319 oligomers on an atomistic scale are proposed.
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Affiliation(s)
- Xikun Liu
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Shuya Duan
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Yingying Jin
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Ethan Walker
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Michelle Tsao
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Joshua H Jang
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Ziying Chen
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Ambuj K Singh
- Department of Computer Science, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Kristi Lazar Cantrell
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Helgi I Ingolfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Steven K Buratto
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael T Bowers
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
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4
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Lantz C, Lopez J, Goring AK, Zenaidee MA, Biggs K, Whitelegge JP, Ogorzalek Loo RR, Klärner FG, Schrader T, Bitan G, Loo JA. Characterization of Molecular Tweezer Binding on α-Synuclein with Native Top-Down Mass Spectrometry and Ion Mobility-Mass Spectrometry Reveals a Mechanism for Aggregation Inhibition. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2739-2747. [PMID: 37936057 PMCID: PMC10959575 DOI: 10.1021/jasms.3c00281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Parkinson's disease, a neurodegenerative disease that affects 15 million people worldwide, is characterized by deposition of α-synuclein into Lewy Bodies in brain neurons. Although this disease is prevalent worldwide, a therapy or cure has yet to be found. Several small compounds have been reported to disrupt fibril formation. Among these compounds is a molecular tweezer known as CLR01 that targets lysine and arginine residues. This study aims to characterize how CLR01 interacts with various proteoforms of α-synuclein and how the structure of α-synuclein is subsequently altered. Native mass spectrometry (nMS) measurements of α-synuclein/CLR01 complexes reveal that multiple CLR01 molecules can bind to α-synuclein proteoforms such as α-synuclein phosphorylated at Ser-129 and α-synuclein bound with copper and manganese ions. The binding of one CLR01 molecule shifts the ability for α-synuclein to bind other ligands. Electron capture dissociation (ECD) with Fourier transform-ion cyclotron resonance (FT-ICR) top-down (TD) mass spectrometry of α-synuclein/CLR01 complexes pinpoints the locations of the modifications on each proteoform and reveals that CLR01 binds to the N-terminal region of α-synuclein. CLR01 binding compacts the gas-phase structure of α-synuclein, as shown by ion mobility-mass spectrometry (IM-MS). These data suggest that when multiple CLR01 molecules bind, the N-terminus of α-synuclein shifts toward a more compact state. This compaction suggests a mechanism for CLR01 halting the formation of oligomers and fibrils involved in many neurodegenerative diseases.
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Affiliation(s)
- Carter Lantz
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Jaybree Lopez
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Andrew K. Goring
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Muhammad A. Zenaidee
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW, Australia
| | - Karl Biggs
- Department of Neurology and Brain Research Institute, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Julian P. Whitelegge
- The Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Rachel R. Ogorzalek Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | | | - Thomas Schrader
- Institute of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Gal Bitan
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW, Australia
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, 90095 USA
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, 90095 USA
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Los Angeles, CA 90095 USA
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Taha HB, Chawla E, Bitan G. IM-MS and ECD-MS/MS Provide Insight into Modulation of Amyloid Proteins Self-Assembly by Peptides and Small Molecules. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2066-2086. [PMID: 37607351 DOI: 10.1021/jasms.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Neurodegenerative proteinopathies are characterized by formation and deposition of misfolded, aggregated proteins in the nervous system leading to neuronal dysfunction and death. It is widely believed that metastable oligomers of the offending proteins, preceding the fibrillar aggregates found in the tissue, are the proximal neurotoxins. There are currently almost no disease-modifying therapies for these diseases despite an active pipeline of preclinical development and clinical trials for over two decades, largely because studying the metastable oligomers and their interaction with potential therapeutics is notoriously difficult. Mass spectrometry (MS) is a powerful analytical tool for structural investigation of proteins, including protein-protein and protein-ligand interactions. Specific MS tools have been useful in determining the composition and conformation of abnormal protein oligomers involved in proteinopathies and the way they interact with drug candidates. Here, we analyze critically the utilization of ion-mobility spectroscopy-MS (IM-MS) and electron-capture dissociation (ECD) MS/MS for analyzing the oligomerization and conformation of multiple amyloidogenic proteins. We also discuss IM-MS investigation of their interaction with two classes of compounds developed by our group over the last two decades: C-terminal fragments derived from the 42-residue form of amyloid β-protein (Aβ42) and molecular tweezers. Finally, we review the utilization of ECD-MS/MS for elucidating the binding sites of the ligands on multiple proteins. These approaches are readily applicable to future studies addressing similar questions and hold promise for facilitating the development of successful disease-modifying drugs against neurodegenerative proteinopathies.
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Affiliation(s)
- Hash Brown Taha
- Department of Neurology, University of California Los Angeles, California 90095, United States
- Department of Integrative Biology & Physiology, University of California Los Angeles, California 90095, United States
| | - Esha Chawla
- Department of Neurology, University of California Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, California 90095, United States
| | - Gal Bitan
- Department of Neurology, University of California Los Angeles, California 90095, United States
- Brain Research Institute, University of California Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California Los Angeles, California 90095, United States
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6
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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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Liu Z, Chen X, Yang S, Tian R, Wang F. Integrated mass spectrometry strategy for functional protein complex discovery and structural characterization. Curr Opin Chem Biol 2023; 74:102305. [PMID: 37071953 DOI: 10.1016/j.cbpa.2023.102305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 04/20/2023]
Abstract
The discovery of functional protein complex and the interrogation of the complex structure-function relationship (SFR) play crucial roles in the understanding and intervention of biological processes. Affinity purification-mass spectrometry (AP-MS) has been proved as a powerful tool in the discovery of protein complexes. However, validation of these novel protein complexes as well as elucidation of their molecular interaction mechanisms are still challenging. Recently, native top-down MS (nTDMS) is rapidly developed for the structural analysis of protein complexes. In this review, we discuss the integration of AP-MS and nTDMS in the discovery and structural characterization of functional protein complexes. Further, we think the emerging artificial intelligence (AI)-based protein structure prediction is highly complementary to nTDMS and can promote each other. We expect the hybridization of integrated structural MS with AI prediction to be a powerful workflow in the discovery and SFR investigation of functional protein complexes.
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Affiliation(s)
- Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiong Chen
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shirui Yang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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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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9
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Samanta N, Ruiz‐Blanco YB, Fetahaj Z, Gnutt D, Lantz C, Loo JA, Sanchez‐Garcia E, Ebbinghaus S. Superoxide Dismutase 1 Folding Stability as a Target for Molecular Tweezers in SOD1-Related Amyotrophic Lateral Sclerosis. Chembiochem 2022; 23:e202200396. [PMID: 36083789 PMCID: PMC9828543 DOI: 10.1002/cbic.202200396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/09/2022] [Indexed: 01/12/2023]
Abstract
Protein misfolding and aggregation are hallmarks of many severe neurodegenerative diseases including Alzheimer's, Parkinson's and Huntington's disease. As a supramolecular ligand that binds to lysine and arginine residues, the molecular tweezer CLR01 was found to modify the aggregation pathway of disease-relevant proteins in vitro and in vivo with beneficial effects on toxicity. However, the molecular mechanisms of how tweezers exert these effects remain mainly unknown, hampering further drug development. Here, we investigate the modulation mechanism of unfolding and aggregation pathways of SOD1, which are involved in amyotrophic lateral sclerosis (ALS), by CLR01. Using a truncated version of the wildtype SOD1 protein, SOD1bar , we show that CLR01 acts on the first step of the aggregation pathway, the unfolding of the SOD1 monomer. CLR01 increases, by ∼10 °C, the melting temperatures of the A4V and G41D SOD1 mutants, which are commonly observed mutations in familial ALS. Molecular dynamics simulations and binding free energy calculations as well as native mass spectrometry and mutational studies allowed us to identify K61 and K92 as binding sites for the tweezers to mediate the stability increase. The data suggest that the modulation of SOD1 conformational stability is a promising target for future developments of supramolecular ligands against neurodegenerative diseases.
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Affiliation(s)
- Nirnay Samanta
- Institute of Physical and Theoretical ChemistryTU Braunschweig38106BraunschweigGermany,Braunschweig Integrated Centre of Systems Biology (BRICS) 38106BraunschweigGermany
| | - Yasser B. Ruiz‐Blanco
- Computational Biochemistry, Center of Medical BiotechnologyUniversity of Duisburg-Essen45141EssenGermany
| | - Zamira Fetahaj
- Department of Physical Chemistry IIRuhr University44780BochumGermany
| | - David Gnutt
- Institute of Physical and Theoretical ChemistryTU Braunschweig38106BraunschweigGermany,Braunschweig Integrated Centre of Systems Biology (BRICS) 38106BraunschweigGermany,Department of Physical Chemistry IIRuhr University44780BochumGermany
| | - Carter Lantz
- Department of Chemistry and BiochemistryUniversity of California-Los Angeles90095Los Angeles, CAUSA
| | - Joseph A. Loo
- Department of Chemistry and BiochemistryUniversity of California-Los Angeles90095Los Angeles, CAUSA
| | - Elsa Sanchez‐Garcia
- Computational Biochemistry, Center of Medical BiotechnologyUniversity of Duisburg-Essen45141EssenGermany
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical ChemistryTU Braunschweig38106BraunschweigGermany,Braunschweig Integrated Centre of Systems Biology (BRICS) 38106BraunschweigGermany,Department of Physical Chemistry IIRuhr University44780BochumGermany
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10
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Le MH, Taghuo-Kaptouom E, Schrader T. Molecular Tweezers – a new class of potent broad-spectrum antivirals against enveloped viruses. Chem Commun (Camb) 2022; 58:2954-2966. [DOI: 10.1039/d1cc06737k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new supramolecular approach to broad spectrum antivirals utilizes host guest chemistry between molecular tweezers and lysine/arginine as well as choline. Basic amino acids in amyloid-forming SEVI peptides (semen-derived enhancers...
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11
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Bennett JL, Nguyen GTH, Donald WA. Protein-Small Molecule Interactions in Native Mass Spectrometry. Chem Rev 2021; 122:7327-7385. [PMID: 34449207 DOI: 10.1021/acs.chemrev.1c00293] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Small molecule drug discovery has been propelled by the continual development of novel scientific methodologies to occasion therapeutic advances. Although established biophysical methods can be used to obtain information regarding the molecular mechanisms underlying drug action, these approaches are often inefficient, low throughput, and ineffective in the analysis of heterogeneous systems including dynamic oligomeric assemblies and proteins that have undergone extensive post-translational modification. Native mass spectrometry can be used to probe protein-small molecule interactions with unprecedented speed and sensitivity, providing unique insights into polydisperse biomolecular systems that are commonly encountered during the drug discovery process. In this review, we describe potential and proven applications of native MS in the study of interactions between small, drug-like molecules and proteins, including large multiprotein complexes and membrane proteins. Approaches to quantify the thermodynamic and kinetic properties of ligand binding are discussed, alongside a summary of gas-phase ion activation techniques that have been used to interrogate the structure of protein-small molecule complexes. We additionally highlight some of the key areas in modern drug design for which native mass spectrometry has elicited significant advances. Future developments and applications of native mass spectrometry in drug discovery workflows are identified, including potential pathways toward studying protein-small molecule interactions on a whole-proteome scale.
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Affiliation(s)
- Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
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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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Malishev R, Salinas N, Gibson J, Eden AB, Mieres-Perez J, Ruiz-Blanco YB, Malka O, Kolusheva S, Klärner FG, Schrader T, Sanchez-Garcia E, Wang C, Landau M, Bitan G, Jelinek R. Inhibition of Staphylococcus aureus biofilm-forming functional amyloid by molecular tweezers. Cell Chem Biol 2021; 28:1310-1320.e5. [PMID: 33852903 DOI: 10.1016/j.chembiol.2021.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/19/2021] [Accepted: 03/19/2021] [Indexed: 02/07/2023]
Abstract
Biofilms are rigid and largely impenetrable three-dimensional matrices constituting virulence determinants of various pathogenic bacteria. Here, we demonstrate that molecular tweezers, unique supramolecular artificial receptors, modulate biofilm formation of Staphylococcus aureus. In particular, the tweezers affect the structural and assembly properties of phenol-soluble modulin α1 (PSMα1), a biofilm-scaffolding functional amyloid peptide secreted by S. aureus. The data reveal that CLR01, a diphosphate tweezer, exhibits significant S. aureus biofilm inhibition and disrupts PSMα1 self-assembly and fibrillation, likely through inclusion of lysine side chains of the peptide. In comparison, different peptide binding occurs in the case of CLR05, a tweezer containing methylenecarboxylate units, which exhibits lower affinity for the lysine residues yet disrupts S. aureus biofilm more strongly than CLR01. Our study points to a possible role for molecular tweezers as potent biofilm inhibitors and antibacterial agents, particularly against untreatable biofilm-forming and PSM-producing bacteria, such as methicillin-resistant S. aureus.
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Affiliation(s)
- Ravit Malishev
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Nir Salinas
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - James Gibson
- Center for Biotechnology and Interdisciplinary Studies, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Angela Bailey Eden
- Center for Biotechnology and Interdisciplinary Studies, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Joel Mieres-Perez
- Department of Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Yasser B Ruiz-Blanco
- Department of Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Orit Malka
- 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
| | | | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Elsa Sanchez-Garcia
- Department of Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; European Molecular Biology Laboratory (EMBL), 22607 Hamburg, Germany
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, Brain Research Institute, and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - 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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14
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Wells C, Brennan S, Keon M, Ooi L. The role of amyloid oligomers in neurodegenerative pathologies. Int J Biol Macromol 2021; 181:582-604. [PMID: 33766600 DOI: 10.1016/j.ijbiomac.2021.03.113] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/18/2021] [Accepted: 03/19/2021] [Indexed: 11/25/2022]
Abstract
Many neurodegenerative diseases are rooted in the activities of amyloid-like proteins which possess conformations that spread to healthy proteins. These include Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD) and amyotrophic lateral sclerosis (ALS). While their clinical manifestations vary, their protein-level mechanisms are remarkably similar. Aberrant monomeric proteins undergo conformational shifts, facilitating aggregation and formation of solid fibrils. However, there is growing evidence that intermediate oligomeric stages are key drivers of neuronal toxicity. Analysis of protein dynamics is complicated by the fact that nucleation and growth of amyloid-like proteins is not a linear pathway. Feedback within this pathway results in exponential acceleration of aggregation, but activities exerted by oligomers and fibrils can alter cellular interactions and the cellular environment as a whole. The resulting cascade of effects likely contributes to the late onset and accelerating progression of amyloid-like protein disorders and the widespread effects they have on the body. In this review we explore the amyloid-like proteins associated with AD, PD, HD and ALS, as well as the common mechanisms of amyloid-like protein nucleation and aggregation. From this, we identify core elements of pathological progression which have been targeted for therapies, and which may become future therapeutic targets.
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Affiliation(s)
- Cameron Wells
- GenieUs Genomics, Sydney, NSW 2010, Australia; University of New South Wales, Sydney, NSW 2052, Australia
| | | | - Matt Keon
- GenieUs Genomics, Sydney, NSW 2010, Australia
| | - Lezanne Ooi
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia; School of Chemistry and Molecular Bioscience, and Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia; GenieUs Genomics, Sydney, NSW 2010, Australia
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15
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Beveridge R, Calabrese AN. Structural Proteomics Methods to Interrogate the Conformations and Dynamics of Intrinsically Disordered Proteins. Front Chem 2021; 9:603639. [PMID: 33791275 PMCID: PMC8006314 DOI: 10.3389/fchem.2021.603639] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/19/2021] [Indexed: 12/21/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and regions of intrinsic disorder (IDRs) are abundant in proteomes and are essential for many biological processes. Thus, they are often implicated in disease mechanisms, including neurodegeneration and cancer. The flexible nature of IDPs and IDRs provides many advantages, including (but not limited to) overcoming steric restrictions in binding, facilitating posttranslational modifications, and achieving high binding specificity with low affinity. IDPs adopt a heterogeneous structural ensemble, in contrast to typical folded proteins, making it challenging to interrogate their structure using conventional tools. Structural mass spectrometry (MS) methods are playing an increasingly important role in characterizing the structure and function of IDPs and IDRs, enabled by advances in the design of instrumentation and the development of new workflows, including in native MS, ion mobility MS, top-down MS, hydrogen-deuterium exchange MS, crosslinking MS, and covalent labeling. Here, we describe the advantages of these methods that make them ideal to study IDPs and highlight recent applications where these tools have underpinned new insights into IDP structure and function that would be difficult to elucidate using other methods.
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Affiliation(s)
- Rebecca Beveridge
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Antonio N. Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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16
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Rahman MU, Rehman AU, Arshad T, Chen HF. Disaggregation mechanism of prion amyloid for tweezer inhibitor. Int J Biol Macromol 2021; 176:510-519. [PMID: 33607137 DOI: 10.1016/j.ijbiomac.2021.02.094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/08/2021] [Accepted: 02/13/2021] [Indexed: 02/07/2023]
Abstract
The aggregation of amyloid has been an important event in the pathology of amyloidogenicity. A number of small molecules have been designed for Amyloidosis treatment. Molecular tweezer CLR01, a potential drug for misfolded β-amyloids inhibition, was reportedly bind directly to Lysine residues and interrupt oligomerization. However, the disaggregation mechanism of amyloid for this inhibitor is unclear. Here we used long timescale of molecular dynamic simulation to reveal the mechanism of disaggregation for pentamer prion amyloid. Molecular docking and molecular dynamics simulation demonstrate that CLR01 is attached with Lysine222 nitrogen by π-cation interaction of its nine aromatic rings and formation of salt bridge/hydrogen bond of one of the two rotatable peripheral anionic phosphate groups. Upon CLR01 binding, we found a major shifting occurs in initial conformation of the oligomer and stretch out the N-terminal chain A from the rest of the amyloid which seems to be the first stage of disaggregated the fibrils slowly yet efficiently. Moreover, the CLR01 remodelled the pentamer Prion220-272 into a compact structure which might be the resistant conformation for further oligomerization. Our work will contribute to better understand the interaction and deterioration mechanism of molecular tweezer for prions and similar amyloids, and offer significant insights into therapeutic development for Amyloidosis treatment.
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Affiliation(s)
- Mueed Ur Rahman
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ashfaq Ur Rehman
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Taaha Arshad
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Center for Bioinformation Technology, Shanghai 200235, China.
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17
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Di J, Siddique I, Li Z, Malki G, Hornung S, Dutta S, Hurst I, Ishaaya E, Wang A, Tu S, Boghos A, Ericsson I, Klärner FG, Schrader T, Bitan G. The molecular tweezer CLR01 improves behavioral deficits and reduces tau pathology in P301S-tau transgenic mice. ALZHEIMERS RESEARCH & THERAPY 2021; 13:6. [PMID: 33397489 PMCID: PMC7784007 DOI: 10.1186/s13195-020-00743-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Molecular tweezers (MTs) are broad-spectrum inhibitors of abnormal protein aggregation. A lead MT, called CLR01, has been demonstrated to inhibit the aggregation and toxicity of multiple amyloidogenic proteins in vitro and in vivo. Previously, we evaluated the effect of CLR01 in the 3 × Tg mouse model of Alzheimer's disease, which overexpresses mutant human presenilin 1, amyloid β-protein precursor, and tau and found that subcutaneous administration of the compound for 1 month led to a robust reduction of amyloid plaques, neurofibrillary tangles, and microgliosis. CLR01 also has been demonstrated to inhibit tau aggregation in vitro and tau seeding in cell culture, yet because in Alzheimer's disease (AD) and in the 3 × Tg model, tau hyperphosphorylation and aggregation are thought to be downstream of Aβ insults, the study in this model left open the question whether CLR01 affected tau in vivo directly or indirectly. METHODS To determine if CLR01 could ameliorate tau pathology directly in vivo, we tested the compound similarly using the P301S-tau (line PS19) mouse model. Mice were administered 0.3 or 1.0 mg/kg per day CLR01 and tested for muscle strength and behavioral deficits, including anxiety- and disinhibition-like behavior. Their brains then were analyzed by immunohistochemical and biochemical assays for pathological forms of tau, neurodegeneration, and glial pathology. RESULTS CLR01 treatment ameliorated muscle-strength deterioration, anxiety-, and disinhibition-like behavior. Improved phenotype was associated with decreased levels of pathologic tau forms, suggesting that CLR01 exerts a direct effect on tau in vivo. Limitations of the study included a relatively short treatment period of the mice at an age in which full pathology is not yet developed. In addition, high variability in this model lowered the statistical significance of the findings of some outcome measures. CONCLUSIONS The findings suggest that CLR01 is a particularly attractive candidate for the treatment of AD because it targets simultaneously the two major pathogenic proteins instigating and propagating the disease, amyloid β-protein (Aβ), and tau, respectively. In addition, our study suggests that CLR01 can be used for the treatment of other tauopathies in the absence of amyloid pathology.
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Affiliation(s)
- Jing Di
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Ibrar Siddique
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Zizheng Li
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Ghattas Malki
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Simon Hornung
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA.,Present Address: Division of Peptide Biochemistry, Technical University of Munich, Freising, Germany
| | - Suman Dutta
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Ian Hurst
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Ella Ishaaya
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Austin Wang
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Sally Tu
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Ani Boghos
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | - Ida Ericsson
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA
| | | | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, University of California, Gordon Neuroscience Research Building, Room 451, 635 Charles E. Young Drive South, Los Angeles, CA, 90095-7334, USA. .,Brain Research Institute, University of California, Los Angeles, CA, USA. .,Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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18
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Bayer P, Matena A, Beuck C. NMR Spectroscopy of supramolecular chemistry on protein surfaces. Beilstein J Org Chem 2020; 16:2505-2522. [PMID: 33093929 PMCID: PMC7554676 DOI: 10.3762/bjoc.16.203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/18/2020] [Indexed: 01/17/2023] Open
Abstract
As one of the few analytical methods that offer atomic resolution, NMR spectroscopy is a valuable tool to study the interaction of proteins with their interaction partners, both biomolecules and synthetic ligands. In recent years, the focus in chemistry has kept expanding from targeting small binding pockets in proteins to recognizing patches on protein surfaces, mostly via supramolecular chemistry, with the goal to modulate protein–protein interactions. Here we present NMR methods that have been applied to characterize these molecular interactions and discuss the challenges of this endeavor.
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Affiliation(s)
- Peter Bayer
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Anja Matena
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
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19
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Lieblein T, Zangl R, Martin J, Hoffmann J, Hutchison MJ, Stark T, Stirnal E, Schrader T, Schwalbe H, Morgner N. Structural rearrangement of amyloid-β upon inhibitor binding suppresses formation of Alzheimer's disease related oligomers. eLife 2020; 9:59306. [PMID: 33095161 PMCID: PMC7682991 DOI: 10.7554/elife.59306] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/22/2020] [Indexed: 01/24/2023] Open
Abstract
The formation of oligomers of the amyloid-β peptide plays a key role in the onset of Alzheimer's disease. We describe herein the investigation of disease-relevant small amyloid-β oligomers by mass spectrometry and ion mobility spectrometry, revealing functionally relevant structural attributes. In particular, we can show that amyloid-β oligomers develop in two distinct arrangements leading to either neurotoxic oligomers and fibrils or non-toxic amorphous aggregates. Comprehending the key-attributes responsible for those pathways on a molecular level is a pre-requisite to specifically target the peptide's tertiary structure with the aim to promote the emergence of non-toxic aggregates. Here, we show for two fibril inhibiting ligands, an ionic molecular tweezer and a hydrophobic peptide that despite their different interaction mechanisms, the suppression of the fibril pathway can be deduced from the disappearance of the corresponding structure of the first amyloid-β oligomers.
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Affiliation(s)
- Tobias Lieblein
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
| | - Rene Zangl
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
| | - Janosch Martin
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
| | - Jan Hoffmann
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
| | - Marie J Hutchison
- JW Goethe-University, Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany
| | - Tina Stark
- JW Goethe-University, Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany
| | - Elke Stirnal
- JW Goethe-University, Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany
| | - Thomas Schrader
- University of Duisburg-Essen, Institute of Organic Chemistry, Essen, Germany
| | - Harald Schwalbe
- JW Goethe-University, Institute for Organic Chemistry and Chemical Biology and Center for Biomolecular Magnetic Resonance, Frankfurt am Main, Germany
| | - Nina Morgner
- JW Goethe-University, Institute of Physical and Theoretical Chemistry, Frankfurt, Germany
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20
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Issa AA, Obayes HR. Capture carcinogenic aromatic compounds by the design of new tweezer compounds: a theoretical study. J Mol Model 2020; 26:292. [PMID: 32995930 DOI: 10.1007/s00894-020-04558-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 09/21/2020] [Indexed: 11/25/2022]
Abstract
Both [5]-circulene and [7]-circulene can be selected to design the molecular tweezers theoretically using the DFT method. Leaning on the cyclic polymerization mechanism, we obtain four new tweezer compounds. Theoretical results offer that tweezer compound (I) is additionally stable than other compounds because it has better energies than other compounds. The values were as follows: - 2606.83372937 a.u. for the total energy, - 5.39820 eV for (EHOMO), and 2.87407 eV for gap energy. The thermodynamic theoretical outcome showed that all reactions are exothermic and spontaneous, suggesting that tweezer compound (I) might correlate with several aromatic compounds, such as pyrene, benzo[ghi]perylene, ovalene, and hexabenzocoronene. The correlation energy results showed an increase as the aromatic compound becomes larger, while the correlation distance decreases. All correlation energy kinds are electrostatic. The value of the electrostatic correlation energy of tweezer compound (I)-ovalene is (- 6.4928615 kJ mol-1). The tweezer compound (I) has a spherical cavity equal to 3.73640 nm3, which adds an important application in the ability to capture chemicals, bacteria, or viruses that are close to the size of the cavity with ease.
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Affiliation(s)
- Ali Abdullah Issa
- Applied Chemistry Division, Applied Science Department, University of Technology, Baghdad, Iraq
| | - Hasan R Obayes
- Applied Chemistry Division, Applied Science Department, University of Technology, Baghdad, Iraq.
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21
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Weil T, Groß R, Röcker A, Bravo-Rodriguez K, Heid C, Sowislok A, Le MH, Erwin N, Dwivedi M, Bart SM, Bates P, Wettstein L, Müller JA, Harms M, Sparrer K, Ruiz-Blanco YB, Stürzel CM, von Einem J, Lippold S, Read C, Walther P, Hebel M, Kreppel F, Klärner FG, Bitan G, Ehrmann M, Weil T, Winter R, Schrader T, Shorter J, Sanchez-Garcia E, Münch J. Supramolecular Mechanism of Viral Envelope Disruption by Molecular Tweezers. J Am Chem Soc 2020; 142:17024-17038. [PMID: 32926779 PMCID: PMC7523239 DOI: 10.1021/jacs.0c06400] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Broad-spectrum
antivirals are powerful weapons against dangerous
viruses where no specific therapy exists, as in the case of the ongoing
SARS-CoV-2 pandemic. We discovered that a lysine- and arginine-specific
supramolecular ligand (CLR01) destroys enveloped viruses, including
HIV, Ebola, and Zika virus, and remodels amyloid fibrils in semen
that promote viral infection. Yet, it is unknown how CLR01 exerts
these two distinct therapeutic activities. Here, we delineate a novel
mechanism of antiviral activity by studying the activity of tweezer
variants: the “phosphate tweezer” CLR01, a “carboxylate
tweezer” CLR05, and a “phosphate clip” PC. Lysine
complexation inside the tweezer cavity is needed to antagonize amyloidogenesis
and is only achieved by CLR01. Importantly, CLR01 and CLR05 but not
PC form closed inclusion complexes with lipid head groups of viral
membranes, thereby altering lipid orientation and increasing surface
tension. This process disrupts viral envelopes and diminishes infectivity
but leaves cellular membranes intact. Consequently, CLR01 and CLR05
display broad antiviral activity against all enveloped viruses tested,
including herpesviruses, Measles virus, influenza, and SARS-CoV-2.
Based on our mechanistic insights, we potentiated the antiviral, membrane-disrupting
activity of CLR01 by introducing aliphatic ester arms into each phosphate
group to act as lipid anchors that promote membrane targeting. The
most potent ester modifications harbored unbranched C4 units, which
engendered tweezers that were approximately one order of magnitude
more effective than CLR01 and nontoxic. Thus, we establish the mechanistic
basis of viral envelope disruption by specific tweezers and establish
a new class of potential broad-spectrum antivirals with enhanced activity.
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Affiliation(s)
- Tatjana Weil
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Annika Röcker
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Kenny Bravo-Rodriguez
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Christian Heid
- Faculty of Chemistry, University of Duisburg-Essen, 45117 Essen, Germany
| | - Andrea Sowislok
- Faculty of Chemistry, University of Duisburg-Essen, 45117 Essen, Germany
| | - My-Hue Le
- Faculty of Chemistry, University of Duisburg-Essen, 45117 Essen, Germany
| | - Nelli Erwin
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Mridula Dwivedi
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Stephen M Bart
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Paul Bates
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Lukas Wettstein
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Konstantin Sparrer
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Jens von Einem
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Sina Lippold
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Clarissa Read
- Institute of Virology, Ulm University Medical Center, 89081 Ulm, Germany.,Central Facility for Electron Microscopy, Ulm University, 89081 Ulm, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, 89081 Ulm, Germany
| | - Marco Hebel
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.,Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Florian Kreppel
- Center for Biomedical Education and Research, University of Witten/Herdecke, Stockumer Strasse 10, 58453 Witten, Germany
| | | | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, Brain Research Institute, and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Michael Ehrmann
- Microbiology II, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.,Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, 45117 Essen, Germany
| | - James Shorter
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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22
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Mitra G. Emerging Role of Mass Spectrometry-Based Structural Proteomics in Elucidating Intrinsic Disorder in Proteins. Proteomics 2020; 21:e2000011. [PMID: 32959512 DOI: 10.1002/pmic.202000011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 06/30/2020] [Indexed: 12/14/2022]
Abstract
Inherent disorder is an integral part of all proteomes, represented as fully or partially unfolded proteins. The lack of order in intrinsically disordered proteins (IDPs) results in an incredibly flexible, floppy, and heterogeneous ensemble, contrary to the well-structured and unique organization of folded proteins. Despite such unusual demeanor, IDPs are crucial for numerous cellular processes and are increasingly being associated with disease-causing pathologies. These warrant more intensive investigation of this atypical class of protein. Traditional biophysical tools, however, fall short of analyzing IDPs, thus making their structure-function characterization challenging. Mass spectrometry (MS) in recent years has evolved as a valuable tool for elucidating the unusual conformational facets of IDPs. In this review, the features of advanced MS techniques such as Hydrogen-deuterium exchange (HDX)-MS, native MS, limited proteolysis (LiP)-MS, chemical cross-linking (XL)-MS, and Fast photochemical oxidation of proteins (FPOP)-MS are briefly discussed. Recent MS studies on IDPs and the unique advantages/shortfalls associated with the above methods while evaluating structural proteomics of IDPs, are illustrated. Eventually the future scope of the MS methods in further decoding the unexplored landscapes of IDPs is presented.
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Affiliation(s)
- Gopa Mitra
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute, St John's Medical College, St. John's National Academy of Health Sciences, 100 Feet Road, Koramangala, Bangalore, Karnataka, 560034, India
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23
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Wiglenda T, Groenke N, Hoffmann W, Manz C, Diez L, Buntru A, Brusendorf L, Neuendorf N, Schnoegl S, Haenig C, Schmieder P, Pagel K, Wanker EE. Sclerotiorin Stabilizes the Assembly of Nonfibrillar Abeta42 Oligomers with Low Toxicity, Seeding Activity, and Beta-sheet Content. J Mol Biol 2020; 432:2080-2098. [PMID: 32061932 DOI: 10.1016/j.jmb.2020.01.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/14/2020] [Accepted: 01/28/2020] [Indexed: 01/21/2023]
Abstract
The self-assembly of the 42-residue amyloid-β peptide, Aβ42, into fibrillar aggregates is associated with neuronal dysfunction and toxicity in Alzheimer's disease (AD) patient brains, suggesting that small molecules acting on this process might interfere with pathogenesis. Here, we present experimental evidence that the small molecule sclerotiorin (SCL), a natural product belonging to the group of azaphilones, potently delays both seeded and nonseeded Aβ42 polymerization in cell-free assays. Mechanistic biochemical studies revealed that the inhibitory effect of SCL on fibrillogenesis is caused by its ability to kinetically stabilize small Aβ42 oligomers. These structures exhibit low β-sheet content and do not possess seeding activity, indicating that SCL acts very early in the amyloid formation cascade before the assembly of seeding-competent, β-sheet-rich fibrillar aggregates. Investigations with NMR WaterLOGSY experiments confirmed the association of Aβ42 assemblies with SCL in solution. Furthermore, using ion mobility-mass spectrometry, we observed that SCL directly interacts with a small fraction of Aβ42 monomers in the gas phase. In comparison to typical amyloid fibrils, small SCL-stabilized Aβ42 assemblies are inefficiently taken up into mammalian cells and have low toxicity in cell-based assays. Overall, these mechanistic studies support a pathological role of stable, β-sheet-rich Aβ42 fibrils in AD, while structures with low β-sheet content may be less relevant.
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Affiliation(s)
- Thomas Wiglenda
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Nicole Groenke
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Waldemar Hoffmann
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Christian Manz
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Lisa Diez
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Alexander Buntru
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Lydia Brusendorf
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Nancy Neuendorf
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Sigrid Schnoegl
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Christian Haenig
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Peter Schmieder
- Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - Kevin Pagel
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Erich E Wanker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
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24
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Pilkington AW, Schupp J, Nyman M, Valentine SJ, Smith DM, Legleiter J. Acetylation of Aβ 40 Alters Aggregation in the Presence and Absence of Lipid Membranes. ACS Chem Neurosci 2020; 11:146-161. [PMID: 31834770 DOI: 10.1021/acschemneuro.9b00483] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A hallmark of Alzheimer's disease (AD) is the formation of senile plaques comprised of the β-amyloid (Aβ) peptide. Aβ fibrillization is a complex nucleation-dependent process involving a variety of metastable intermediate aggregates and features the formation of inter- and intramolecular salt bridges involving lysine residues, K16 and K28. Cationic lysine residues also mediate protein-lipid interactions via association with anionic lipid headgroups. As several toxic mechanisms attributed to Aβ involve membrane interactions, the impact of acetylation on Aβ40 aggregation in the presence and absence of membranes was determined. Using chemical acetylation, varying mixtures of acetylated and nonacetylated Aβ40 were produced. With increasing acetylation, fibril and oligomer formation decreased, eventually completely arresting fibrillization. In the presence of total brain lipid extract (TBLE) vesicles, acetylation reduced the interaction of Aβ40 with membranes; however, fibrils still formed at near complete levels of acetylation. Additionally, the combination of TBLE and acetylated Aβ promoted annular aggregates. Finally, toxicity associated with Aβ40 was reduced with increasing acetylation in a cell culture assay. These results suggest that in the absence of membranes that the cationic character of lysine plays a major role in fibril formation. However, acetylation promotes unique aggregation pathways in the presence of lipid membranes.
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Affiliation(s)
- Albert W. Pilkington
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Jane Schupp
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Morgan Nyman
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Stephen J. Valentine
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - David M. Smith
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, United States
- Rockefeller Neurosciences Institutes, West Virginia University, 1 Medical Center Drive, P.O. Box 9303, Morgantown, West Virginia 26505, United States
- Department of Neuroscience, West Virginia University, 1 Medical Center Drive, P.O. Box
9303, Morgantown, West Virginia 26505, United States
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry, West Virginia University, 217 Clark Hall, Morgantown, West Virginia 26506, United States
- Rockefeller Neurosciences Institutes, West Virginia University, 1 Medical Center Drive, P.O. Box 9303, Morgantown, West Virginia 26505, United States
- Department of Neuroscience, West Virginia University, 1 Medical Center Drive, P.O. Box
9303, Morgantown, West Virginia 26505, United States
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25
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De Simone A, Naldi M, Tedesco D, Bartolini M, Davani L, Andrisano V. Advanced analytical methodologies in Alzheimer’s disease drug discovery. J Pharm Biomed Anal 2020; 178:112899. [DOI: 10.1016/j.jpba.2019.112899] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 12/13/2022]
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26
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Laos V, Bishop D, Lang CA, Marsh NM, Cantrell KL, Buratto SK, Singh AK, Bowers MT. Modulating ALS-Related Amyloidogenic TDP-43 307-319 Oligomeric Aggregates with Computationally Derived Therapeutic Molecules. Biochemistry 2019; 59:499-508. [PMID: 31846303 DOI: 10.1021/acs.biochem.9b00905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
TDP-43 aggregates are a salient feature of amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and a variety of other neurodegenerative diseases, including Alzheimer's disease (AD). With an anticipated growth in the most susceptible demographic, projections predict neurodegenerative diseases will potentially affect 15 million people in the United States by 2050. Currently, there are no cures for ALS, FTD, or AD. Previous studies of the amyloidogenic core of TDP-43 have demonstrated that oligomers greater than a trimer are associated with toxicity. Utilizing a joint pharmacophore space (JPS) method, potential drugs have been designed specifically for amyloid-related diseases. These molecules were generated on the basis of key chemical features necessary for blood-brain barrier permeability, low adverse side effects, and target selectivity. Combining ion-mobility mass spectrometry and atomic force microscopy with the JPS computational method allows us to more efficiently evaluate a potential drug's efficacy in disrupting the development of putative toxic species. Our results demonstrate the dissociation of higher-order oligomers in the presence of these novel JPS-generated inhibitors into smaller oligomer species. Additionally, drugs approved by the Food and Drug Administration for the treatment of ALS were also evaluated and demonstrated to maintain higher-order oligomeric assemblies. Possible mechanisms for the observed action of the JPS molecules are discussed.
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Affiliation(s)
- Veronica Laos
- Department of Chemistry & Biochemistry , University of California, Santa Barbara , Santa Barbara , California 93106 , United States
| | - Dezmond Bishop
- Department of Chemistry & Biochemistry , University of California, Santa Barbara , Santa Barbara , California 93106 , United States
| | | | - Nicole M Marsh
- Department of Chemistry , Westmont College , Santa Barbaraa , California 93108 , United States
| | - Kristi Lazar Cantrell
- Department of Chemistry , Westmont College , Santa Barbaraa , California 93108 , United States
| | - Steven K Buratto
- Department of Chemistry & Biochemistry , University of California, Santa Barbara , Santa Barbara , California 93106 , United States
| | - Ambuj K Singh
- Department of Computer Science , University of California, Santa Barbara , Santa Barbara , California 93106-5110 , United States
| | - Michael T Bowers
- Department of Chemistry & Biochemistry , University of California, Santa Barbara , Santa Barbara , California 93106 , United States
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27
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Kumari N, Yadav S. Modulation of protein oligomerization: An overview. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 149:99-113. [DOI: 10.1016/j.pbiomolbio.2019.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 12/21/2022]
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28
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Pyo AGT, Woodside MT. Memory effects in single-molecule force spectroscopy measurements of biomolecular folding. Phys Chem Chem Phys 2019; 21:24527-24534. [PMID: 31663550 DOI: 10.1039/c9cp04197d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Folding is generally assumed to be a Markov process, without memory. When the molecular motion is coupled to that of a probe as in single-molecule force spectroscopy (SMFS) experiments, however, theory predicts that the coupling to a second Markov process should induce memory when monitoring a projection of the full multi-dimensional motion onto a reduced coordinate. We developed a method to evaluate the time constant of the induced memory from its effects on the autocorrelation function, which can be readily determined from experimental data. Applying this method to both simulated SMFS measurements and experimental trajectories of DNA hairpin folding measured by optical tweezers as a model system, we validated the prediction that the linker induces memory. For these measurements, the timescale of the induced memory was found to be similar to the time required for the force probe to respond to changes in the molecule, and in the regime where the experimentally observed dynamics were not significantly perturbed by probe-molecule coupling artifacts. Memory effects are thus a general feature of SMFS measurements induced by the mechanical connection between the molecule and force probe that should be considered when interpreting experimental data.
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Affiliation(s)
- Andrew G T Pyo
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada.
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29
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Han JY, Choi TS, Heo CE, Son MK, Kim HI. Gas-phase conformations of intrinsically disordered proteins and their complexes with ligands: Kinetically trapped states during transfer from solution to the gas phase. MASS SPECTROMETRY REVIEWS 2019; 38:483-500. [PMID: 31021441 DOI: 10.1002/mas.21596] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
Flexible structures of intrinsically disordered proteins (IDPs) are crucial for versatile functions in living organisms, which involve interaction with diverse partners. Electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) has been widely applied for structural characterization of apo-state and ligand-associated IDPs via two-dimensional separation in the gas phase. Gas-phase IDP structures have been regarded as kinetically trapped states originated from conformational features in solution. However, an implication of the states remains elusive in the structural characterization of IDPs, because it is unclear what structural property of IDPs is preserved. Recent studies have indicated that the conformational features of IDPs in solution are not fully reproduced in the gas phase. Nevertheless, the molecular interactions captured in the gas phase amplify the structural differences between IDP conformers. Therefore, an IDP conformational change that is not observed in solution is observable in the gas-phase structures obtained by ESI-IM-MS. Herein, we have presented up-to-date researches on the key implications of kinetically trapped states in the gas phase with a brief summary of the structural dynamics of IDPs in ESI-IM-MS.
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Affiliation(s)
- Jong Yoon Han
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Tae Su Choi
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093
| | - Chae Eun Heo
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Myung Kook Son
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
| | - Hugh I Kim
- Department of Chemistry, Korea University, Seoul, 02841, Republic of Korea
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30
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Hadrovic I, Rebmann P, Klärner FG, Bitan G, Schrader T. Molecular Lysine Tweezers Counteract Aberrant Protein Aggregation. Front Chem 2019; 7:657. [PMID: 31632951 PMCID: PMC6779714 DOI: 10.3389/fchem.2019.00657] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/13/2019] [Indexed: 01/10/2023] Open
Abstract
Molecular tweezers (MTs) are supramolecular host molecules equipped with two aromatic pincers linked together by a spacer (Gakh, 2018). They are endowed with fascinating properties originating from their ability to hold guests between their aromatic pincers (Chen and Whitlock, 1978; Zimmerman, 1991; Harmata, 2004). MTs are finding an increasing number of medicinal applications, e.g., as bis-intercalators for DNA such as the anticancer drug Ditercalinium (Gao et al., 1991), drug activity reverters such as the bisglycoluril tweezers Calabadion 1 (Ma et al., 2012) as well as radioimmuno detectors such as Venus flytrap clusters (Paxton et al., 1991). We recently embarked on a program to create water-soluble tweezers which selectively bind the side chains of lysine and arginine inside their cavity. This unique recognition mode is enabled by a torus-shaped, polycyclic framework, which is equipped with two hydrophilic phosphate groups. Cationic amino acid residues are bound by the synergistic effect of disperse, hydrophobic, and electrostatic interactions in a kinetically fast reversible process. Interactions of the same kind play a key role in numerous protein-protein interactions, as well as in pathologic protein aggregation. Therefore, these particular MTs show a high potential to disrupt such events, and indeed inhibit misfolding and self-assembly of amyloidogenic polypeptides without toxic side effects. The mini-review provides insight into the unique binding mode of MTs both toward peptides and aggregating proteins. It presents the synthesis of the lead compound CLR01 and its control, CLR03. Different biophysical experiments are explained which elucidate and help to better understand their mechanism of action. Specifically, we show how toxic aggregates of oligomeric and fibrillar protein species are dissolved and redirected to form amorphous, benign assemblies. Importantly, these new chemical tools are shown to be essentially non-toxic in vivo. Due to their reversible moderately tight binding, these agents are not protein-, but rather process-specific, which suggests a broad range of applications in protein misfolding events. Thus, MTs are highly promising candidates for disease-modifying therapy in early stages of neurodegenerative diseases. This is an outstanding example in the evolution of supramolecular concepts toward biological application.
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Affiliation(s)
- Inesa Hadrovic
- Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Philipp Rebmann
- Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | | | - Gal Bitan
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
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31
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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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32
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Mitra G. Application of native mass spectrometry in studying intrinsically disordered proteins: A special focus on neurodegenerative diseases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140260. [PMID: 31382021 DOI: 10.1016/j.bbapap.2019.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 12/26/2022]
Abstract
Intrinsically disordered proteins (IDPs) are integral part of the proteome, regulating vital biological processes. Such proteins gained further visibility due to their key role in neurodegenerative diseases and cancer. IDPs however, escape structural characterization by traditional biophysical tools owing to their extreme flexibility and heterogeneity. In this review, we discuss the advantages of native mass spectrometry (MS) in analysing the atypical conformational dynamics of IDPs and recent advances made in the field. Especially, MS studies unravelling the conformational facets of IDPs involved in neurodegenerative diseases are highlighted. The limitations and the future promises of native MS while studying IDPs have been discussed.
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Affiliation(s)
- Gopa Mitra
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute, St. John's National Academy of Health Sciences, 100 Feet Road, Koramangala, Bangalore 560034, Karnataka, India.
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33
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Despres C, Di J, Cantrelle FX, Li Z, Huvent I, Chambraud B, Zhao J, Chen J, Chen S, Lippens G, Zhang F, Linhardt R, Wang C, Klärner FG, Schrader T, Landrieu I, Bitan G, Smet-Nocca C. Major Differences between the Self-Assembly and Seeding Behavior of Heparin-Induced and in Vitro Phosphorylated Tau and Their Modulation by Potential Inhibitors. ACS Chem Biol 2019; 14:1363-1379. [PMID: 31046227 PMCID: PMC6636790 DOI: 10.1021/acschembio.9b00325] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Self-assembly of
the microtubule-associated protein tau into neurotoxic
oligomers, fibrils, and paired helical filaments, and cell-to-cell
spreading of these pathological tau species are critical processes
underlying the pathogenesis of Alzheimer’s disease and other
tauopathies. Modulating the self-assembly process and inhibiting formation
and spreading of such toxic species are promising strategies for therapy
development. A challenge in investigating tau self-assembly in vitro
is that, unlike most amyloidogenic proteins, tau does not aggregate
in the absence of posttranslational modifications (PTM), aggregation
inducers, or preformed seeds. The most common induction method is
addition of polyanions, such as heparin; yet, this artificial system
may not represent adequately tau self-assembly in vivo, which is driven
by aberrant phosphorylation and other PTMs, potentially leading to
in vitro data that do not reflect the behavior of tau and its interaction
with modulators in vivo. To tackle these challenges, methods for in
vitro phosphorylation of tau to produce aggregation-competent forms
recently have been introduced (Despres
et al. (2017) Proc. Natl. Acad. Sci. U.S.A., 114, 9080−908528784767). However, the oligomerization, seeding, and interaction
with assembly modulators of the different forms of tau have not been
studied to date. To address these knowledge gaps, we compared here
side-by-side the self-assembly and seeding activity of heparin-induced
tau with two forms of in vitro phosphorylated tau and tested how the
molecular tweezer CLR01, a negatively charged compound, affected these
processes. Tau was phosphorylated by incubation either with activated
extracellular signal-regulated kinase 2 or with a whole rat brain
extract. Seeding activity was measured using a fluorescence-resonance
energy transfer-based biosensor-cell method. We also used solution-state
NMR to investigate the binding sites of CLR01 on tau and how they
were impacted by phosphorylation. Our systematic structure–activity
relationship study demonstrates that heparin-induced tau behaves differently
from in vitro phosphorylated tau. The aggregation rates of the different
forms are distinct as is the intracellular localization of the induced
aggregates, which resemble brain-derived tau strains suggesting that
heparin-induced tau and in vitro phosphorylated tau have different
conformations, properties, and activities. CLR01 inhibits aggregation
and seeding of both heparin-induced and in vitro phosphorylated tau
dose-dependently, although heparin induction interferes with the interaction
between CLR01 and tau.
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Affiliation(s)
| | | | | | | | | | | | | | - Jianle Chen
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Shiguo Chen
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Guy Lippens
- Lille University CNRS UMR 8576, UGSF, F-59000 Lille, France
| | | | - Robert Linhardt
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | | | - Frank-Gerrit Klärner
- Institute of Organic Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
| | - Thomas Schrader
- Institute of Organic Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
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34
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Malik R, Meng H, Wongkongkathep P, Corrales CI, Sepanj N, Atlasi RS, Klärner FG, Schrader T, Spencer MJ, Loo JA, Wiedau M, Bitan G. The molecular tweezer CLR01 inhibits aberrant superoxide dismutase 1 (SOD1) self-assembly in vitro and in the G93A-SOD1 mouse model of ALS. J Biol Chem 2019; 294:3501-3513. [PMID: 30602569 DOI: 10.1074/jbc.ra118.005940] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/01/2019] [Indexed: 12/13/2022] Open
Abstract
Mutations in superoxide dismutase 1 (SOD1) cause 15-20% of familial amyotrophic lateral sclerosis (fALS) cases. The resulting amino acid substitutions destabilize SOD1's protein structure, leading to its self-assembly into neurotoxic oligomers and aggregates, a process hypothesized to cause the characteristic motor-neuron degeneration in affected individuals. Currently, effective disease-modifying therapy is not available for ALS. Molecular tweezers prevent formation of toxic protein assemblies, yet their protective action has not been tested previously on SOD1 or in the context of ALS. Here, we tested the molecular tweezer CLR01-a broad-spectrum inhibitor of the self-assembly and toxicity of amyloid proteins-as a potential therapeutic agent for ALS. Using recombinant WT and mutant SOD1, we found that CLR01 inhibited the aggregation of all tested SOD1 forms in vitro Next, we examined whether CLR01 could prevent the formation of misfolded SOD1 in the G93A-SOD1 mouse model of ALS and whether such inhibition would have a beneficial therapeutic effect. CLR01 treatment decreased misfolded SOD1 in the spinal cord significantly. However, these histological findings did not correlate with improvement of the disease phenotype. A small, dose-dependent decrease in disease duration was found in CLR01-treated mice, relative to vehicle-treated animals, yet motor function did not improve in any of the treatment groups. These results demonstrate that CLR01 can inhibit SOD1 misfolding and aggregation both in vitro and in vivo, but raise the question whether such inhibition is sufficient for achieving a therapeutic effect. Additional studies in other less aggressive ALS models may be needed to determine the therapeutic potential of this approach.
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Affiliation(s)
- Ravinder Malik
- From the Department of Neurology, David Geffen School of Medicine, and
| | - Helen Meng
- From the Department of Neurology, David Geffen School of Medicine, and
| | | | | | - Niki Sepanj
- From the Department of Neurology, David Geffen School of Medicine, and
| | - Ryan S Atlasi
- From the Department of Neurology, David Geffen School of Medicine, and
| | | | - Thomas Schrader
- the Faculty of Chemistry, University of Duisburg-Essen, 47057 Essen, Germany
| | - Melissa J Spencer
- From the Department of Neurology, David Geffen School of Medicine, and.,Brain Research Institute, and
| | - Joseph A Loo
- Departments of Chemistry and Biochemistry and.,Biological Chemistry.,Molecular Biology Institute, UCLA, Los Angeles, California 90095 and
| | - Martina Wiedau
- From the Department of Neurology, David Geffen School of Medicine, and .,Brain Research Institute, and
| | - Gal Bitan
- From the Department of Neurology, David Geffen School of Medicine, and .,Brain Research Institute, and.,Molecular Biology Institute, UCLA, Los Angeles, California 90095 and
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35
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36
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Downey MA, Giammona MJ, Lang CA, Buratto SK, Singh A, Bowers MT. Inhibiting and Remodeling Toxic Amyloid-Beta Oligomer Formation Using a Computationally Designed Drug Molecule That Targets Alzheimer's Disease. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:85-93. [PMID: 29713966 PMCID: PMC6258352 DOI: 10.1007/s13361-018-1975-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 05/25/2023]
Abstract
Alzheimer's disease (AD) is rapidly reaching epidemic status among a burgeoning aging population. Much evidence suggests the toxicity of this amyloid disease is most influenced by the formation of soluble oligomeric forms of amyloid β-protein, particularly the 42-residue alloform (Aβ42). Developing potential therapeutics in a directed, streamlined approach to treating this disease is necessary. Here we utilize the joint pharmacophore space (JPS) model to design a new molecule [AC0107] incorporating structural characteristics of known Aβ inhibitors, blood-brain barrier permeability, and limited toxicity. To test the molecule's efficacy experimentally, we employed ion mobility mass spectrometry (IM-MS) to discover [AC0107] inhibits the formation of the toxic Aβ42 dodecamer at both high (1:10) and equimolar concentrations of inhibitor. Atomic force microscopy (AFM) experiments reveal that [AC0107] prevents further aggregation of Aβ42, destabilizes preformed fibrils, and reverses Aβ42 aggregation. This trend continues for long-term interaction times of 2 days until only small aggregates remain with virtually no fibrils or higher order oligomers surviving. Pairing JPS with IM-MS and AFM presents a powerful and effective first step for AD drug development. Graphical Abstract.
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Affiliation(s)
- Matthew A Downey
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Maxwell J Giammona
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Christian A Lang
- Acelot, Inc., 5385 Hollister Ave, Suite 111, Santa Barbara, CA, 93111, USA
| | - Steven K Buratto
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Ambuj Singh
- Acelot, Inc., 5385 Hollister Ave, Suite 111, Santa Barbara, CA, 93111, USA
- Department of Computer Science, University of California, Santa Barbara, CA, 93106, USA
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA.
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37
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Nshanian M, Lantz C, Wongkongkathep P, Schrader T, Klärner FG, Blümke A, Despres C, Ehrmann M, Smet-Nocca C, Bitan G, Loo JA. Native Top-Down Mass Spectrometry and Ion Mobility Spectrometry of the Interaction of Tau Protein with a Molecular Tweezer Assembly Modulator. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:16-23. [PMID: 30062477 PMCID: PMC6320309 DOI: 10.1007/s13361-018-2027-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 07/03/2018] [Accepted: 07/03/2018] [Indexed: 05/19/2023]
Abstract
Native top-down mass spectrometry (MS) and ion mobility spectrometry (IMS) were applied to characterize the interaction of a molecular tweezer assembly modulator, CLR01, with tau, a protein believed to be involved in a number of neurodegenerative disorders, including Alzheimer's disease. The tweezer CLR01 has been shown to inhibit aggregation of amyloidogenic polypeptides without toxic side effects. ESI-MS spectra for different forms of tau protein (full-length, fragments, phosphorylated, etc.) in the presence of CLR01 indicate a primary binding stoichiometry of 1:1. The relatively high charging of the protein measured from non-denaturing solutions is typical of intrinsically disordered proteins, such as tau. Top-down mass spectrometry using electron capture dissociation (ECD) is a tool used to determine not only the sites of post-translational modifications but also the binding site(s) of non-covalent interacting ligands to biomolecules. The intact protein and the protein-modulator complex were subjected to ECD-MS to obtain sequence information, map phosphorylation sites, and pinpoint the sites of inhibitor binding. The ESI-MS study of intact tau proteins indicates that top-down MS is amenable to the study of various tau isoforms and their post-translational modifications (PTMs). The ECD-MS data point to a CLR01 binding site in the microtubule-binding region of tau, spanning residues K294-K331, which includes a six-residue nucleating segment PHF6 (VQIVYK) implicated in aggregation. Furthermore, ion mobility experiments on the tau fragment in the presence of CLR01 and phosphorylated tau reveal a shift towards a more compact structure. The mass spectrometry study suggests a picture for the molecular mechanism of the modulation of protein-protein interactions in tau by CLR01. Graphical Abstract ᅟ.
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Affiliation(s)
- Michael Nshanian
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Carter Lantz
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Piriya Wongkongkathep
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Thomas Schrader
- Institute of Chemistry, University of Duisburg-Essen, Essen, Germany
| | | | - Anika Blümke
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Universitaetsstrasse, Essen, Germany
| | - Clément Despres
- UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Université Lille, CNRS, 59000, Lille, France
| | - Michael Ehrmann
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Universitaetsstrasse, Essen, Germany
| | - Caroline Smet-Nocca
- UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Université Lille, CNRS, 59000, Lille, France
| | - Gal Bitan
- Department of Neurology and Brain Research Institute, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
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38
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Kikot LS, Kulygina CY, Lyapunov AY, Shishkina SV, Zubatyuk RI, Bogashchenko TY, Kirichenko TI. Synthesis and complexation of molecular clips based on diphenylglycoluril and dibenzocrown ethers with alkali metal cations and paraquat. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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39
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Röcker A, Roan NR, Yadav JK, Fändrich M, Münch J. Structure, function and antagonism of semen amyloids. Chem Commun (Camb) 2018; 54:7557-7569. [PMID: 29873340 DOI: 10.1039/c8cc01491d] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Amyloid fibrils are linear polypeptide aggregates with a cross-β structure. These fibrils are best known for their association with neurodegenerative diseases, such as Alzheimer's or Parkinson's, but they may also be used by living organisms as functional units, e.g. in the synthesis of melanin or in the formation of bacterial biofilms. About a decade ago, in a search for semen factors that modulate infection by HIV-1 (a sexually transmitted virus and the causative agent of the acquired immune deficiency syndrome (AIDS)), it was demonstrated that semen harbors amyloid fibrils capable of markedly increasing HIV infection rates. This discovery not only created novel opportunities to prevent sexual HIV-1 transmission but also stimulated research to unravel the natural role of these factors. We discuss here the identification of these intriguing structures, their molecular properties, and their effects on both sexually transmitted diseases and reproductive health. Moreover, we review strategies to antagonize semen amyloid to prevent sexual transmission of viruses.
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Affiliation(s)
- Annika Röcker
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany.
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40
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Mittal S, Bravo-Rodriguez K, Sanchez-Garcia E. Mechanism of Inhibition of Beta Amyloid Toxicity by Supramolecular Tweezers. J Phys Chem B 2018; 122:4196-4205. [DOI: 10.1021/acs.jpcb.7b10530] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sumit Mittal
- University of Duisburg-Essen, Universitätsstraße 2, 45141 Essen, Germany
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41
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Wang JSH, Whitehead SN, Yeung KKC. Detection of Amyloid Beta (Aβ) Oligomeric Composition Using Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI MS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:786-795. [PMID: 29464543 DOI: 10.1007/s13361-018-1896-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/16/2018] [Accepted: 01/16/2018] [Indexed: 06/08/2023]
Abstract
The use of MALDI MS as a fast and direct method to detect the Aβ oligomers of different masses is examined in this paper. Experimental results suggest that Aβ oligomers are ionized and detected as singly charged ions, and thus, the resulting mass spectrum directly reports the oligomer size distribution. Validation experiments were performed to verify the MS data against artifacts. Mass spectra collected from modified Aβ peptides with different propensities for aggregation were compared. Generally, the relative intensities of multimers were higher from samples where oligomerization was expected to be more favorable, and vice versa. MALDI MS was also able to detect the differences in oligomeric composition before and after the incubation/oligomerization step. Such differences in sample composition were also independently confirmed with an in vitro Aβ toxicity study on primary rat cortical neurons. An additional validation was accomplished through removal of oligomers from the sample using molecular weight cutoff filters; the resulting MS data correctly reflected the removal at the expected cutoff points. The results collectively validated the ability of MALDI MS to assess the monomeric/multimeric composition of Aβ samples. Graphical Abstract ᅟ.
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Affiliation(s)
- Jasmine S-H Wang
- Department of Chemistry, University of Western Ontario, London, ON, N6A 5B7, Canada
- Department of Biochemistry, University of Western Ontario, London, ON, N6A 5C1, Canada
- Vulnerable Brain Laboratory, Department of Anatomy and Cell Biology, University of Western Ontario, London, ON, N6A 5C1, Canada
| | - Shawn N Whitehead
- Vulnerable Brain Laboratory, Department of Anatomy and Cell Biology, University of Western Ontario, London, ON, N6A 5C1, Canada
| | - Ken K-C Yeung
- Department of Chemistry, University of Western Ontario, London, ON, N6A 5B7, Canada.
- Department of Biochemistry, University of Western Ontario, London, ON, N6A 5C1, Canada.
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42
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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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43
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Malik R, Di J, Nair G, Attar A, Taylor K, Teng E, Klärner FG, Schrader T, Bitan G. Using Molecular Tweezers to Remodel Abnormal Protein Self-Assembly and Inhibit the Toxicity of Amyloidogenic Proteins. Methods Mol Biol 2018; 1777:369-386. [PMID: 29744849 DOI: 10.1007/978-1-4939-7811-3_24] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Molecular tweezers (MTs) are broad-spectrum inhibitors of abnormal protein self-assembly, which act by binding selectively to lysine and arginine residues. Through this unique mechanism of action, MTs inhibit formation of toxic oligomers and aggregates. Their efficacy and safety have been demonstrated in vitro, in cell culture, and in animal models. Here, we discuss the application of MTs in diverse in vitro and in vivo systems, the experimental details, the scope of their use, and the limitations of the approach. We also consider methods for administration of MTs in animal models to measure efficacy, pharmacokinetic, and pharmacodynamic parameters in proteinopathies.
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Affiliation(s)
- Ravinder Malik
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Jing Di
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Gayatri Nair
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Aida Attar
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA.,Brain Research Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - Karen Taylor
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Edmond Teng
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA.,Greater Los Angeles Healthcare System, Veterans Hospital, West Los Angeles, CA, USA
| | | | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA. .,Brain Research Institute, University of California at Los Angeles, Los Angeles, CA, USA. .,Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA, USA.
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44
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Gospodarczyk W, Kozak M. Microchip Circulation Drastically Accelerates Amyloid Aggregation of 1-42 β-amyloid Peptide from Felis catus. ACS Chem Neurosci 2017; 8:2558-2567. [PMID: 28759721 DOI: 10.1021/acschemneuro.7b00285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The amyloid aggregation process of amyloid β1-42 peptide is responsible for Alzheimer's disease, affecting millions of elderly people worldwide. Although there has been a great deal of attention directed toward tackling this disease, still no medicine has been found for this fatal disorder. To address this challenge, it is vital to thoroughly understand the molecular mechanism underlying the amyloid peptide aggregation process, as well as seek substances that could hamper this aggregation. In order to shed light on mechanisms leading to amyloidogenesis, we employed a microfluidic system to determine the possible influence of in vivo-like flow in the microchip channel itself on feline Aβ1-42 peptide amyloidogenesis. We have shown that shear forces occurring during such flow immensely accelerated peptide aggregation. We also tested the inhibitory influence of 3,3'-[1,6-(2,5-dioxahexane)]bis(1-dodecylimidazolium) dichloride gemini surfactant on peptide amyloidogenesis. Our results suggest that this surfactant may inhibit amyloid β1-42 fibril formation.
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Affiliation(s)
- Witold Gospodarczyk
- Department of Macromolecular
Physics, Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Maciej Kozak
- Department of Macromolecular
Physics, Faculty of Physics, Adam Mickiewicz University, 61-614 Poznań, Poland
- Joint Laboratory
for SAXS studies, Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań, Poland
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45
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Ion mobility-mass spectrometry and orthogonal gas-phase techniques to study amyloid formation and inhibition. Curr Opin Struct Biol 2017; 46:7-15. [DOI: 10.1016/j.sbi.2017.03.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/28/2017] [Accepted: 03/03/2017] [Indexed: 11/24/2022]
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46
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de Almeida NEC, Do TD, LaPointe NE, Tro M, Feinstein SC, Shea JE, Bowers MT. 1,2,3,4,6-penta-O-galloyl-β-D-glucopyranose Binds to the N-terminal Metal Binding Region to Inhibit Amyloid β-protein Oligomer and Fibril Formation. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2017; 420:24-34. [PMID: 29056865 PMCID: PMC5644501 DOI: 10.1016/j.ijms.2016.09.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The early oligomerization of amyloid β-protein (Aβ) is a crucial step in the etiology of Alzheimer's disease (AD), in which soluble and highly neurotoxic oligomers are produced and accumulated inside neurons. In search of therapeutic solutions for AD treatment and prevention, potent inhibitors that remodel Aβ assembly and prevent neurotoxic oligomer formation offer a promising approach. In particular, several polyphenolic compounds have shown anti-aggregation properties and good efficacy on inhibiting oligomeric amyloid formation. 1,2,3,4,6-penta-O-galloyl-β-D-glucopyranose is a large polyphenol that has been shown to be effective at inhibiting aggregation of full-length Aβ1-40 and Aβ1-42, but has the opposite effect on the C-terminal fragment Aβ25-35. Here, we use a combination of ion mobility coupled to mass spectrometry (IMS-MS), transmission electron microscopy (TEM) and molecular dynamics (MD) simulations to elucidate the inhibitory effect of PGG on aggregation of full-length Aβ1-40 and Aβ1-42. We show that PGG interacts strongly with these two peptides, especially in their N-terminal metal binding regions, and suppresses the formation of Aβ1-40 tetramer and Aβ1-42 dodecamer. By exploring multiple facets of polyphenol-amyloid interactions, we provide a molecular basis for the opposing effects of PGG on full-length Aβ and its C-terminal fragments.
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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 the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, 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
| | - Michael Tro
- Department of Chemistry and Biochemistry, 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
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Xu N, Bitan G, Schrader T, Klärner FG, Osinska H, Robbins J. Inhibition of Mutant αB Crystallin-Induced Protein Aggregation by a Molecular Tweezer. J Am Heart Assoc 2017; 6:JAHA.117.006182. [PMID: 28862927 PMCID: PMC5586456 DOI: 10.1161/jaha.117.006182] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Compromised protein quality control causes the accumulation of misfolded proteins and intracellular aggregates, contributing to cardiac disease and heart failure. The development of therapeutics directed at proteotoxicity‐based pathology in heart disease is just beginning. The molecular tweezer CLR01 is a broad‐spectrum inhibitor of abnormal self‐assembly of amyloidogenic proteins, including amyloid β‐protein, tau, and α‐synuclein. This small molecule interferes with aggregation by binding selectively to lysine side chains, changing the charge distribution of aggregation‐prone proteins and thereby disrupting aggregate formation. However, the effects of CLR01 in cardiomyocytes undergoing proteotoxic stress have not been explored. Here we assess whether CLR01 can decrease cardiac protein aggregation catalyzed by cardiomyocyte‐specific expression of mutated αB‐crystallin (CryABR120G). Methods and Results A proteotoxic model of desmin‐related cardiomyopathy caused by cardiomyocyte‐specific expression of CryABR120G was used to test the efficacy of CLR01 therapy in the heart. Neonatal rat cardiomyocytes were infected with adenovirus expressing either wild‐type CryAB or CryABR120G. Subsequently, the cells were treated with different doses of CLR01 or a closely related but inactive derivative, CLR03. CLR01 decreased aggregate accumulation and attenuated cytotoxicity caused by CryABR120G expression in a dose‐dependent manner, whereas CLR03 had no effect. Ubiquitin‐proteasome system function was analyzed using a ubiquitin‐proteasome system reporter protein consisting of a short degron, CL1, fused to the COOH‐terminus of green fluorescent protein. CLR01 improved proteasomal function in CryABR120G cardiomyocytes but did not alter autophagic flux. In vivo, CLR01 administration also resulted in reduced protein aggregates in CryABR120G transgenic mice. Conclusions CLR01 can inhibit CryABR120G aggregate formation and decrease cytotoxicity in cardiomyocytes undergoing proteotoxic stress, presumably through clearance of the misfolded protein via increased proteasomal function. CLR01 or related compounds may be therapeutically useful in treating the pathogenic sequelae resulting from proteotoxic heart disease.
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Affiliation(s)
- Na Xu
- Division of Molecular Cardiovascular Biology, the Heart Institute, Cincinnati Children's Hospital, Cincinnati, OH
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, Brain Research Institute, and Molecular Biology Institute, University of California at Los Angeles, CA
| | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | | | - Hanna Osinska
- Division of Molecular Cardiovascular Biology, the Heart Institute, Cincinnati Children's Hospital, Cincinnati, OH
| | - Jeffrey Robbins
- Division of Molecular Cardiovascular Biology, the Heart Institute, Cincinnati Children's Hospital, Cincinnati, OH
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48
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Porrini M, Rosu F, Rabin C, Darré L, Gómez H, Orozco M, Gabelica V. Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry. ACS CENTRAL SCIENCE 2017; 3:454-461. [PMID: 28573208 PMCID: PMC5445532 DOI: 10.1021/acscentsci.7b00084] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Indexed: 05/25/2023]
Abstract
We report on the fate of nucleic acids conformation in the gas phase as sampled using native mass spectrometry coupled to ion mobility spectrometry. On the basis of several successful reports for proteins and their complexes, the technique has become popular in structural biology, and the conformation survival becomes more and more taken for granted. Surprisingly, we found that DNA and RNA duplexes, at the electrospray charge states naturally obtained from native solution conditions (≥100 mM aqueous NH4OAc), are significantly more compact in the gas phase compared to the canonical solution structures. The compaction is observed for all duplex sizes (gas-phase structures are more compact than canonical B-helices by ∼20% for 12-bp, and by up to ∼30% for 36-bp duplexes), and for DNA and RNA alike. Molecular modeling (density functional calculations on small helices, semiempirical calculations on up to 12-bp, and molecular dynamics on up to 36-bp duplexes) demonstrates that the compaction is due to phosphate group self-solvation prevailing over Coulomb repulsion. Molecular dynamics simulations starting from solution structures do not reproduce the experimental compaction. To be experimentally relevant, molecular dynamics sampling should reflect the progressive structural rearrangements occurring during desolvation. For nucleic acid duplexes, the compaction observed for low charge states results from novel phosphate-phosphate hydrogen bonds formed across both grooves at the very late stages of electrospray.
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Affiliation(s)
- Massimiliano Porrini
- INSERM,
CNRS, Université de Bordeaux, Acides
Nucléiques Régulations Naturelle et Artificielle (ARNA,
U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Frédéric Rosu
- CNRS,
INSERM, Université de Bordeaux, Institut
Européen de Chimie et Biologie (IECB, UMS3033, US001), 2 rue Robert Escarpit, 33607 Pessac, France
| | - Clémence Rabin
- INSERM,
CNRS, Université de Bordeaux, Acides
Nucléiques Régulations Naturelle et Artificielle (ARNA,
U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Leonardo Darré
- The
Barcelona Institute of Science and Technology, Institute for Research in Biomedicine (IRB) Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
- Joint
BSC-CRG-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain
| | - Hansel Gómez
- The
Barcelona Institute of Science and Technology, Institute for Research in Biomedicine (IRB) Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
- Joint
BSC-CRG-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain
| | - Modesto Orozco
- The
Barcelona Institute of Science and Technology, Institute for Research in Biomedicine (IRB) Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
- Joint
BSC-CRG-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain
- Department
of Biochemistry and Biomedicine, University
of Barcelona, Avda Diagonal
647, 08028 Barcelona, Spain
| | - Valérie Gabelica
- INSERM,
CNRS, Université de Bordeaux, Acides
Nucléiques Régulations Naturelle et Artificielle (ARNA,
U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France
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Vöpel T, Bravo-Rodriguez K, Mittal S, Vachharajani S, Gnutt D, Sharma A, Steinhof A, Fatoba O, Ellrichmann G, Nshanian M, Heid C, Loo JA, Klärner FG, Schrader T, Bitan G, Wanker EE, Ebbinghaus S, Sanchez-Garcia E. Inhibition of Huntingtin Exon-1 Aggregation by the Molecular Tweezer CLR01. J Am Chem Soc 2017; 139:5640-5643. [PMID: 28406616 DOI: 10.1021/jacs.6b11039] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Huntington's disease is a neurodegenerative disorder associated with the expansion of the polyglutamine tract in the exon-1 domain of the huntingtin protein (htte1). Above a threshold of 37 glutamine residues, htte1 starts to aggregate in a nucleation-dependent manner. A 17-residue N-terminal fragment of htte1 (N17) has been suggested to play a crucial role in modulating the aggregation propensity and toxicity of htte1. Here we identify N17 as a potential target for novel therapeutic intervention using the molecular tweezer CLR01. A combination of biochemical experiments and computer simulations shows that binding of CLR01 induces structural rearrangements within the htte1 monomer and inhibits htte1 aggregation, underpinning the key role of N17 in modulating htte1 toxicity.
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Affiliation(s)
- Tobias Vöpel
- Department of Physical Chemistry II, Ruhr-University Bochum , 44780 Bochum, Germany
| | | | - Sumit Mittal
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Shivang Vachharajani
- Department of Physical Chemistry II, Ruhr-University Bochum , 44780 Bochum, Germany
| | - David Gnutt
- Department of Physical Chemistry II, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Abhishek Sharma
- Department of Physical Chemistry II, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Anne Steinhof
- Max Delbrück Center for Molecular Medicine , 13125 Berlin, Germany
| | - Oluwaseun Fatoba
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Gisa Ellrichmann
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Michael Nshanian
- Department of Chemistry and Biochemistry, University of California at Los Angeles , Los Angeles, California 90095, United States
| | - Christian Heid
- Institute of Organic Chemistry, University of Duisburg-Essen , 45141 Essen, Germany
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California at Los Angeles , Los Angeles, California 90095, United States.,Department of Biological Chemistry and UCLA/DOE Institute of Genomics and Proteomics, University of California at Los Angeles , Los Angeles, California 90095, United States
| | - Frank-Gerrit Klärner
- Institute of Organic Chemistry, University of Duisburg-Essen , 45141 Essen, Germany
| | - Thomas Schrader
- Institute of Organic Chemistry, University of Duisburg-Essen , 45141 Essen, 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 90095-7334, United States
| | - Erich E Wanker
- Max Delbrück Center for Molecular Medicine , 13125 Berlin, Germany
| | - Simon Ebbinghaus
- Department of Physical Chemistry II, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Elsa Sanchez-Garcia
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
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50
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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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