Structure-Based Approach Yields Tau Inhibitors

Since amyloid fibers are presumed molecular culprits in Alzheimer’s and many other diseases, scientists have worked to find or create molecules that block growth of these peptide assemblies. Many endeavors relied more on luck and intuition than on rational design, in part because it is hard to determine the structure of amyloidogenic proteins. Now, in a June 15 Nature paper published online, researchers show that with structural insight they can build highly specific peptide inhibitors of tau fibrillization. “It’s the first structure-based design of a fibrillization inhibitor,” said lead investigator David Eisenberg of the University of California at Los Angeles. Though the compounds have not been tested in a biological system, the research hints that a structure-based approach to limiting fibrillization may work for a variety of amyloid-forming proteins.

Without firm data on amyloid structure, prior efforts to block fibril formation used two basic approaches—screening for molecules that disrupt the process in solution, or devising compounds to interfere with the “sticky” portions of amyloidogenic proteins. “We tried a third approach,” Eisenberg said. “Starting with the atomic structure of a piece of tau protein, we asked what sort of molecule we could build that would cap a tau fiber so it won’t grow any further.”

Reaching the starting point was a feat in itself. Full-length tau does not crystallize, making it impossible to solve its atomic structure. Instead, the researchers focused on previously identified short peptides that drive protein self-aggregation. These short peptides can themselves grow into fibers. Furthermore, some of those hexapeptides formed crystals amenable to structural analysis, revealing an intriguing characteristic of amyloid fibrils: The side chains of hydrophobic amino acids on paired β-sheets interlocked tightly to form “steric zippers” (ARF related news story on Nelson et al., 2005). Tau protein also has these features (Sawaya et al., 2007).

For the current study, Stuart Sievers and colleagues focused on one such zipper—a hexapeptide (VQIVYK) that drives assembly of tau into pathological filaments (von Bergen et al., 2000). With this peptide as a template, Sievers worked with co-first author John Karanicolas of David Baker’s group at the University of Washington, Seattle, to design an inhibitor to cap elongating tau fibers. Howard Chang, Anni Zhao, and Lin Jiang of the Eisenberg lab also contributed equally to the work. The team used software developed in the Baker lab to identify candidate blockers, then showed that they work in solution to slow fibrillization of the template hexapeptide, as well as 150- and 128-residue tau fragments. To improve the inhibitors’ stability, researchers built them using non-natural D-amino acids. “Our bodies are filled with proteases trained to chew up [L-amino acid] peptides that are not normally in cells. That’s why we chose non-natural amino acids,” Eisenberg said. In a recent study, Aβ-binding D-enantiomeric peptides reduced plaque load and improved cognition in AD transgenic mice (Funke et al., 2010), suggesting D-amino acid peptides may be well suited for drug development.

“It’s an awesome protein engineering paper,” said Torleif Härd of the Swedish University of Agricultural Sciences, Uppsala. Dieter Willbold of the Institute of Structural Biology and Biophysics in Jülich, Germany, cited specificity as a key advantage of inhibitors designed using the structure-based approach (see full comment below). Mark Findeis of Satori Pharmaceuticals, Cambridge, Massachusetts, called the work “a really nice step forward,” adding that its methods could be used to design an inhibitor for “anything that has known structural data. You could apply it to models of other proteins, even if you didn’t have firm structural data like what’s available for tau,” he told ARF.

Sievers and colleagues used their computational method to build inhibitors not only for tau fibrils, but also for an amyloidogenic protein (prostatic acid phosphatase) that enhances human immunodeficiency virus (HIV) infection. The latter blocked formation of phosphatase fibrils and, importantly, prevented HIV infection in a functional assay.

The tau inhibitors, on the other hand, are not expected to work in a biological setting because they do not penetrate the brain, Eisenberg said. His group is currently using the inhibitors as tools for finding other tau fibrillization blockers that may be more brain penetrant.

In a PLoS Biology paper published earlier this week (Landau et al., 2011), Eisenberg and colleagues report the first atomic-level structures of small molecules bound to amyloid forms of tau and Aβ. “These pictures begin to map out what’s called the amyloid pharmacophore—a collection of sites on a protein that define how ligands bind to it. That’s a step to drug design,” Eisenberg said.

As for whether blocking fibrillization will be able to help AD patients, only time will tell. Several Aβ aggregation inhibitors have looked promising in Phase 2 trials. One (Elan Corporation’s scyllo-inositol) is heading toward Phase 3 (see ARF related news story). Another (tramiprosate, aka Neurochem’s Alzhemed) failed in a Phase 3 trial (see ARF related news story). Meanwhile, at least one study questions the whole premise by suggesting that some small-molecule amyloid inhibitors work by forming colloids that generally disrupt protein-protein interactions, even the good ones (ARF related news story on Feng et al., 2008).—Esther Landhuis

Comments

  1. Small molecule ligands rationally designed to complement β-sheet hydrogen-bond patterns present in fibrils, but that halt continuation of the β-sheet, e.g., aminopyrazole derivatives, have been known for some time (1,2). These β-sheet-complementing substances, however, lack specificity for fibrils built of a certain protein or peptide.

    Sievers and colleagues report a very elegant study on the rational, 3-dimensional structure-based design of small peptide ligands that specifically bind to their target molecules in fibrillar conformation. Their decisive advantage over the aforementioned β-sheet-complementing substances is specificity. Sievers et al. clearly show that they arrive at peptides that bind specifically and show interesting activities in vitro.

    The researchers combine the advantages of β-sheet-complementing compounds with those of substances that can specifically bind a certain amyloidogenic peptide or protein—more or less irrespective of its conformation.

    Recently, we described a distantly similar approach when we covalently linked a classical β-sheet-complementing substance with a peptide that specifically binds Aβ. The resulting hybrid substance also was very efficient in in-vitro assays (3). D3, the peptide moiety of this hybrid substance is a D-enantiomeric peptide and has already been shown to be very efficient in animal models in vivo, where it reduced the amyloid plaque load and improved cognitive behavior of transgenic mice, even after oral treatment (4).

    This shows that peptides, especially D-enantiomeric peptides, may well be suitable for drug development.

    We look forward to results from in vivo studies of these new peptides. We hope the researchers will be successful. In our view, fighting Alzheimer’s disease and AIDS is worth every effort.

    References:

    Permanne B, Adessi C, Fraga S, Frossard MJ, Saborio GP, Soto C. Are beta-sheet breaker peptides dissolving the therapeutic problem of Alzheimer's disease?. J Neural Transm Suppl. 2002;(62):293-301. PubMed.

    Nagel-Steger L, Demeler B, Meyer-Zaika W, Hochdörffer K, Schrader T, Willbold D. Modulation of aggregate size- and shape-distributions of the amyloid-beta peptide by a designed beta-sheet breaker. Eur Biophys J. 2010 Feb;39(3):415-22. PubMed.

    Müller-Schiffmann A, März-Berberich J, Andreyeva A, Rönicke R, Bartnik D, Brener O, Kutzsche J, Horn AH, Hellmert M, Polkowska J, Gottmann K, Reymann KG, Funke SA, Nagel-Steger L, Moriscot C, Schoehn G, Sticht H, Willbold D, Schrader T, Korth C. Combining independent drug classes into superior, synergistically acting hybrid molecules. Angew Chem Int Ed Engl. 2010 Nov 8;49(46):8743-6. PubMed.

    Aileen Funke S, van Groen T, Kadish I, Bartnik D, Nagel-Steger L, Brener O, Sehl T, Batra-Safferling R, Moriscot C, Schoehn G, Horn AH, Müller-Schiffmann A, Korth C, Sticht H, Willbold D. Oral treatment with the d-enantiomeric peptide D3 improves the pathology and behavior of Alzheimer's Disease transgenic mice. ACS Chem Neurosci. 2010 Sep 15;1(9):639-48. Epub 2010 Aug 2 PubMed.

    View all comments by Susanne Aileen Funke

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References

News Citations

  1. Making Heads and Tails of Prion Amyloid
  2. Anti-Aβ Oligomer Headed for Phase 3 Clinical Trial
  3. FDA Deems U.S. Alzhemed Trial Results Inconclusive
  4. Coll(o)iding With Physical Chemistry: Amyloid Inhibitors Questioned

Paper Citations

  1. Nelson R, Sawaya MR, Balbirnie M, Madsen AØ, Riekel C, Grothe R, Eisenberg D. Structure of the cross-beta spine of amyloid-like fibrils. Nature. 2005 Jun 9;435(7043):773-8. PubMed.
  2. Sawaya MR, Sambashivan S, Nelson R, Ivanova MI, Sievers SA, Apostol MI, Thompson MJ, Balbirnie M, Wiltzius JJ, McFarlane HT, Madsen AØ, Riekel C, Eisenberg D. Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature. 2007 May 24;447(7143):453-7. PubMed.
  3. von Bergen M, Friedhoff P, Biernat J, Heberle J, Mandelkow EM, Mandelkow E. Assembly of tau protein into Alzheimer paired helical filaments depends on a local sequence motif ((306)VQIVYK(311)) forming beta structure. Proc Natl Acad Sci U S A. 2000 May 9;97(10):5129-34. PubMed.
  4. Feng BY, Toyama BH, Wille H, Colby DW, Collins SR, May BC, Prusiner SB, Weissman J, Shoichet BK. Small-molecule aggregates inhibit amyloid polymerization. Nat Chem Biol. 2008 Mar;4(3):197-9. PubMed.

External Citations

  1. Funke et al., 2010
  2. Landau et al., 2011

Further Reading

Papers

  1. Nelson R, Sawaya MR, Balbirnie M, Madsen AØ, Riekel C, Grothe R, Eisenberg D. Structure of the cross-beta spine of amyloid-like fibrils. Nature. 2005 Jun 9;435(7043):773-8. PubMed.
  2. Sawaya MR, Sambashivan S, Nelson R, Ivanova MI, Sievers SA, Apostol MI, Thompson MJ, Balbirnie M, Wiltzius JJ, McFarlane HT, Madsen AØ, Riekel C, Eisenberg D. Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature. 2007 May 24;447(7143):453-7. PubMed.

Primary Papers

  1. Sievers SA, Karanicolas J, Chang HW, Zhao A, Jiang L, Zirafi O, Stevens JT, Münch J, Baker D, Eisenberg D. Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature. 2011 Jul 7;475(7354):96-100. PubMed.

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