Structure based inhibitors of Amyloid Beta core suggest a common interface with Tau

  1. Sarah L Griner  Is a corresponding author
  2. Paul Seidler
  3. Jeannette Bowler
  4. Kevin A Murray
  5. Tianxiao Peter Yang
  6. Shruti Sahay
  7. Michael R Sawaya
  8. Duilio Cascio
  9. Jose A Rodriguez
  10. Stephan Philipp
  11. Justyna Sosna
  12. Charles G Glabe
  13. Tamir Gonen
  14. David S Eisenberg  Is a corresponding author
  1. Howard Hughes Medical Institute, University of California, Los Angeles, United States
  2. University of California, Irvine, United States
  3. Janelia Research Campus, Howard Hughes Medical Institute, United States

Abstract

Alzheimer's disease (AD) pathology is characterized by plaques of amyloid beta (Aβ) and neurofibrillary tangles of tau. Aβ aggregation is thought to occur at early stages of the disease, and ultimately gives way to the formation of tau tangles which track with cognitive decline in humans. Here, we report the crystal structure of an Aβ core segment determined by MicroED and in it, note characteristics of both fibrillar and oligomeric structure. Using this structure, we designed peptide-based inhibitors that reduce Aβ aggregation and toxicity of already-aggregated species. Unexpectedly, we also found that these inhibitors reduce the efficiency of Aβ-mediated tau aggregation, and moreover reduce aggregation and self-seeding of tau fibrils. The ability of these inhibitors to interfere with both Aβ and tau seeds suggests these fibrils share a common epitope, and supports the hypothesis that cross-seeding is one mechanism by which amyloid is linked to tau aggregation and could promote cognitive decline.

Data availability

Diffraction data have been deposited in PDB under the accession code 6O4JSource Data for Toxicity and Seeding data are provided (Figures 2-7)

The following data sets were generated

Article and author information

Author details

  1. Sarah L Griner

    Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
    For correspondence
    sgriner@ucla.edu
    Competing interests
    No competing interests declared.
  2. Paul Seidler

    Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    No competing interests declared.
  3. Jeannette Bowler

    Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    No competing interests declared.
  4. Kevin A Murray

    Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    No competing interests declared.
  5. Tianxiao Peter Yang

    Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4479-5154
  6. Shruti Sahay

    Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    No competing interests declared.
  7. Michael R Sawaya

    Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    No competing interests declared.
  8. Duilio Cascio

    Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    No competing interests declared.
  9. Jose A Rodriguez

    Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    No competing interests declared.
  10. Stephan Philipp

    Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, United States
    Competing interests
    No competing interests declared.
  11. Justyna Sosna

    Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, United States
    Competing interests
    No competing interests declared.
  12. Charles G Glabe

    Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, United States
    Competing interests
    No competing interests declared.
  13. Tamir Gonen

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9254-4069
  14. David S Eisenberg

    Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States
    For correspondence
    david@mbi.ucla.edu
    Competing interests
    David S Eisenberg, is a SAB member and equity holder in ADRx, Inc.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2432-5419

Funding

National Institutes of Health (R01 AG029430)

  • Sarah L Griner
  • Paul Seidler
  • Jeannette Bowler
  • Kevin A Murray
  • Tianxiao Peter Yang
  • Shruti Sahay
  • Michael R Sawaya
  • Duilio Cascio
  • Jose A Rodriguez
  • David S Eisenberg

Howard Hughes Medical Institute

  • Sarah L Griner
  • Paul Seidler
  • Jeannette Bowler
  • Kevin A Murray
  • Tianxiao Peter Yang
  • Shruti Sahay
  • Michael R Sawaya
  • Duilio Cascio
  • Jose A Rodriguez
  • Tamir Gonen
  • David S Eisenberg

Cure Alzheimer's Fund

  • Stephan Philipp
  • Justyna Sosna
  • Charles G Glabe

National Institutes of Health (R56 AG061847)

  • Paul Seidler

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2019, Griner et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 6,007
    views
  • 1,043
    downloads
  • 93
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Sarah L Griner
  2. Paul Seidler
  3. Jeannette Bowler
  4. Kevin A Murray
  5. Tianxiao Peter Yang
  6. Shruti Sahay
  7. Michael R Sawaya
  8. Duilio Cascio
  9. Jose A Rodriguez
  10. Stephan Philipp
  11. Justyna Sosna
  12. Charles G Glabe
  13. Tamir Gonen
  14. David S Eisenberg
(2019)
Structure based inhibitors of Amyloid Beta core suggest a common interface with Tau
eLife 8:e46924.
https://doi.org/10.7554/eLife.46924

Share this article

https://doi.org/10.7554/eLife.46924

Further reading

    1. Biochemistry and Chemical Biology
    2. Computational and Systems Biology
    A Sofia F Oliveira, Fiona L Kearns ... Adrian J Mulholland
    Short Report

    The spike protein is essential to the SARS-CoV-2 virus life cycle, facilitating virus entry and mediating viral-host membrane fusion. The spike contains a fatty acid (FA) binding site between every two neighbouring receptor-binding domains. This site is coupled to key regions in the protein, but the impact of glycans on these allosteric effects has not been investigated. Using dynamical nonequilibrium molecular dynamics (D-NEMD) simulations, we explore the allosteric effects of the FA site in the fully glycosylated spike of the SARS-CoV-2 ancestral variant. Our results identify the allosteric networks connecting the FA site to functionally important regions in the protein, including the receptor-binding motif, an antigenic supersite in the N-terminal domain, the fusion peptide region, and another allosteric site known to bind heme and biliverdin. The networks identified here highlight the complexity of the allosteric modulation in this protein and reveal a striking and unexpected link between different allosteric sites. Comparison of the FA site connections from D-NEMD in the glycosylated and non-glycosylated spike revealed that glycans do not qualitatively change the internal allosteric pathways but can facilitate the transmission of the structural changes within and between subunits.

    1. Biochemistry and Chemical Biology
    2. Genetics and Genomics
    Conor J Howard, Nathan S Abell ... Nathan B Lubock
    Research Article

    Deep Mutational Scanning (DMS) is an emerging method to systematically test the functional consequences of thousands of sequence changes to a protein target in a single experiment. Because of its utility in interpreting both human variant effects and protein structure-function relationships, it holds substantial promise to improve drug discovery and clinical development. However, applications in this domain require improved experimental and analytical methods. To address this need, we report novel DMS methods to precisely and quantitatively interrogate disease-relevant mechanisms, protein-ligand interactions, and assess predicted response to drug treatment. Using these methods, we performed a DMS of the melanocortin-4 receptor (MC4R), a G-protein-coupled receptor (GPCR) implicated in obesity and an active target of drug development efforts. We assessed the effects of >6600 single amino acid substitutions on MC4R’s function across 18 distinct experimental conditions, resulting in >20 million unique measurements. From this, we identified variants that have unique effects on MC4R-mediated Gαs- and Gαq-signaling pathways, which could be used to design drugs that selectively bias MC4R’s activity. We also identified pathogenic variants that are likely amenable to a corrector therapy. Finally, we functionally characterized structural relationships that distinguish the binding of peptide versus small molecule ligands, which could guide compound optimization. Collectively, these results demonstrate that DMS is a powerful method to empower drug discovery and development.