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Title: Structure-based discovery of fiber-binding compounds that reduce the cytotoxicity of amyloid beta

Journal Article · · eLife
DOI:https://doi.org/10.7554/eLife.00857· OSTI ID:1197662
 [1];  [1];  [1];  [1];  [1];  [1];  [1]
  1. Departments of Chemistry and Biochemistry and Biological Chemistry, Howard Hughes Medical Institute, UCLA–DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, United States

Amyloid protein aggregates are associated with dozens of devastating diseases including Alzheimer’s, Parkinson’s, ALS, and diabetes type 2. While structure-based discovery of compounds has been effective in combating numerous infectious and metabolic diseases, ignorance of amyloid structure has hindered similar approaches to amyloid disease. Here we show that knowledge of the atomic structure of one of the adhesive, steric-zipper segments of the amyloid-beta (Aβ) protein of Alzheimer’s disease, when coupled with computational methods, identifies eight diverse but mainly flat compounds and three compound derivatives that reduce Aβ cytotoxicity against mammalian cells by up to 90%. Although these compounds bind to Aβ fibers, they do not reduce fiber formation of Aβ. Structure-activity relationship studies of the fiber-binding compounds and their derivatives suggest that compound binding increases fiber stability and decreases fiber toxicity, perhaps by shifting the equilibrium of Aβ from oligomers to fibers.

Research Organization:
Univ. of California, Los Angeles, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
Grant/Contract Number:
FC02-02ER63421
OSTI ID:
1197662
Alternate ID(s):
OSTI ID: 1197667; OSTI ID: 1628798
Journal Information:
eLife, Journal Name: eLife Vol. 2; ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.Copyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 109 works
Citation information provided by
Web of Science

References (56)

Conserved features of intermediates in amyloid assembly determine their benign or toxic states journal June 2012
Shape Complementarity at Protein/Protein Interfaces journal December 1993
The Amyloid State of Proteins in Human Diseases journal March 2012
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility journal December 2009
Experimental Constraints on Quaternary Structure in Alzheimer's β-Amyloid Fibrils journal January 2006
The Interaction of an Epidermal Growth Factor/Transforming Growth Factor α Tail Chimera with the Human Epidermal Growth Factor Receptor Reveals Unexpected Complexities journal November 1996
Phenolic Compounds Prevent Amyloid β-Protein Oligomerization and Synaptic Dysfunction by Site-specific Binding journal March 2012
EGCG redirects amyloidogenic polypeptides into unstructured, off-pathway oligomers journal May 2008
Imaging brain amyloid in Alzheimer's disease with Pittsburgh Compound-B: Imaging Amyloid in AD with PIB journal January 2004
Amyloid β-sheet mimics that antagonize protein aggregation and reduce amyloid toxicity journal September 2012
RosettaLigand Docking with Full Ligand and Receptor Flexibility journal January 2009
Curcumin Inhibits Formation of Amyloid β Oligomers and Fibrils, Binds Plaques, and Reduces Amyloid in Vivo journal December 2004
Direct Observation of the Interconversion of Normal and Toxic Forms of α-Synuclein journal May 2012
Amyloid-binding compounds maintain protein homeostasis during ageing and extend lifespan journal March 2011
SOGGY: Solvent-optimized double gradient spectroscopy for water suppression. A comparison with some existing techniques journal February 2007
Structural properties of A  protofibrils stabilized by a small molecule journal May 2005
Common Structure of Soluble Amyloid Oligomers Implies Common Mechanism of Pathogenesis journal April 2003
Towards a Pharmacophore for Amyloid journal June 2011
Atomic View of a Toxic Amyloid Small Oligomer journal March 2012
3D structure of Alzheimer's amyloid- (1-42) fibrils journal November 2005
ZINC − A Free Database of Commercially Available Compounds for Virtual Screening journal December 2004
The Amyloid-Congo Red Interface at Atomic Resolution journal May 2011
ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility journal November 2006
Natural oligomers of the amyloid-β protein specifically disrupt cognitive function journal December 2004
Small Molecule Microarrays Enable the Discovery of Compounds That Bind the Alzheimer’s Aβ Peptide and Reduce its Cytotoxicity journal December 2010
The Recombinant Amyloid-β Peptide Aβ1–42 Aggregates Faster and Is More Neurotoxic than Synthetic Aβ1–42 journal February 2010
Inhibition of Alzheimer’s disease β-amyloid aggregation, neurotoxicity, and in vivo deposition by nitrophenols: implications for Alzheimer’s therapy journal May 2001
Out-of-register  -sheets suggest a pathway to toxic amyloid aggregates journal December 2012
The most infectious prion protein particles journal September 2005
Self-Propagating, Molecular-Level Polymorphism in Alzheimer's  -Amyloid Fibrils journal January 2005
Amyloid-β fibrillogenesis: Structural insight and therapeutic intervention journal June 2010
Small Molecule Inhibitors of Aggregation Indicate That Amyloid β Oligomerization and Fibrillization Pathways Are Independent and Distinct journal February 2007
Molecular basis for amyloid-  polymorphism journal September 2011
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases journal May 2001
Peptide and Protein Mimetics Inhibiting Amyloid β-Peptide Aggregation journal October 2008
N-Methylated Peptide Inhibitors of β-Amyloid Aggregation and Toxicity. Optimization of the Inhibitor Structure journal August 2006
Native protein sequences are close to optimal for their structures journal September 2000
Aromatic Small Molecules Remodel Toxic Soluble Oligomers of Amyloid β through Three Independent Pathways journal November 2010
Assessing the performance of OMEGA with respect to retrieving bioactive conformations journal March 2003
Heat Shock Proteins 70 and 90 Inhibit Early Stages of Amyloid β-(1–42) Aggregation in Vitro journal September 2006
Inhibition of Amyloid Formation journal August 2012
Cyclohexanehexol inhibitors of Aβ aggregation prevent and reverse Alzheimer phenotype in a mouse model journal June 2006
Atomic structures of amyloid cross-β spines reveal varied steric zippers journal April 2007
Congo red and protein aggregation in neurodegenerative diseases journal January 2007
Peptide Inhibitors of Beta Amyloid Aggregation journal April 2002
Therapeutic strategies for human amyloid diseases journal April 2002
Microcin Amyloid Fibrils A Are Reservoir of Toxic Oligomeric Species journal February 2012
Rational design of potent domain antibody inhibitors of amyloid fibril assembly journal November 2012
The Blue Obelisk—Interoperability in Chemical Informatics journal May 2006
Inhibition of Amyloid Fibril Formation by Polyphenols: Structural Similarity and Aromatic Interactions as a Common Inhibition Mechanism journal January 2006
Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules book January 2011
Small-molecule conversion of toxic oligomers to nontoxic β-sheet–rich amyloid fibrils journal November 2011
Protein Misfolding, Functional Amyloid, and Human Disease journal June 2006
Strategies for the Inhibition of Protein Aggregation in Human Diseases journal April 2010
Discovery and Structure Activity Relationship of Small Molecule Inhibitors of Toxic β-Amyloid-42 Fibril Formation journal August 2012
Structure of the cross-β spine of amyloid-like fibrils journal June 2005

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