Systematic development of small molecules to inhibit specific microscopic steps of Aβ42 aggregation in Alzheimer’s disease

Abstract

The aggregation of the 42-residue form of the amyloid-β peptide (Aβ42) is a pivotal event in Alzheimer's disease (AD). The use of chemical kinetics has recently enabled highly accurate quantifications of the effects of small molecules on specific microscopic steps in Aβ42 aggregation. Here, we exploit this approach to develop a rational drug discovery strategy against Aβ42 aggregation that uses as a readout the changes in the nucleation and elongation rate constants caused by candidate small molecules. We thus identify a pool of compounds that target specific microscopic steps in Aβ42 aggregation. We then test further these small molecules in human cerebrospinal fluid and in a Caenorhabditis elegans model of AD. Our results show that this strategy represents a powerful approach to identify systematically small molecule lead compounds, thus offering an appealing opportunity to reduce the attrition problem in drug discovery.Alzheimer's disease | amyloid-β peptide | protein misfolding | drug discovery | protein aggregation A lzheimer's disease (AD) is, to date, an incurable neurodegenerative disorder that imposes substantial social and economic costs worldwide (1). According to the amyloid hypothesis, the aggregation of the amyloid-β peptide (Aβ) initiates a cascade of molecular events leading eventually to neuronal death (2-11). Because the presence of abnormal Aβ metabolism can be detected 10-20 years before the onset of AD (12, 13), early interventions may be possible before widespread and irreversible neurodegeneration has occurred. Although targeting Aβ accumulation has been pursued as a major potential therapeutic strategy against AD (14-17), no compound selected for this purpose has yet entered clinical use (18,19).Although these failures have raised doubts about the amyloid hypothesis (20), they can also be attributed to an incomplete knowledge of the molecular mechanisms by which the compounds tested so far affect the nucleation and growth of Aβ aggregates. Indeed, it has been shown that inhibiting Aβ aggregation without a detailed understanding of the underlying microscopic processes could affect the toxicity in unexpected ways (21,22). For example, the inhibition of nucleation events may delay or decrease toxicity, whereas the inhibition of elongation may lead to an overall increase in toxicity (21,22). Therefore, effective therapeutic strategies must be aimed at targeting precise microscopic steps during the Aβ aggregation process (21,(23)(24)(25).We describe here the development of a systematic pipeline based on chemical kinetics to identify a pool of candidate molecules directed against the aggregation of the 42-residue form of Aβ (Aβ42), and to understand the key chemical features responsible for their inhibitory activity. Results and DiscussionA Quasi-Structure-Based Drug Discovery Strategy. We introduce first a quasi-structure-based drug discovery (QSBDD) strategy, which builds on the recent finding that the small molecule bexarotene delays primary nucleation in Aβ42 aggregation (22) (Fig. 1A). Bec...

Conformational Ensembles of the Wild-Type and S8C Aβ1–42 Dimers

“…This study, in concert with recent simulations and experiments on new variants, 56–59 may help design new inhibitors for early-stage Alzheimer disease. 60–62 …”

Selective targeting of primary and secondary nucleation pathways in Aβ42 aggregation using a rational antibody scanning method

“…Seeded experiments were performed in the presence of 10% preformed fibrils ( 23 ) with a 0:1 or 1:1 antibody–to–Aβ42 monomer ratio. Each sample was then pipetted into multiple wells of a 96-well half-area plate of black polystyrene with a clear bottom and polyethylene glycol coating (Corning) (90 μl per well).…”

Reactive Amphiphilic Conjugated Polymers for Inhibiting Amyloid β Assembly

“…[1][2][3][4][5][6][7] On this account, numerous approaches to inhibit amyloid assembly have emerged, ranging from synthetic and natural small-molecule compounds, [4,8,9] peptides, [10,11] antibodies, [12] and nanoparticles [13,14] to artificial chaperones, [15] which make certain achievements to the inhibition of pathogenic aggregates.H owever,t od ate,t he pharmacological treatments for these diseases are still unsatisfactory. Inhibition of amyloid assembly is apromising strategy for the treatment of amyloidosis.R eported here is the design and synthesis of areactive conjugated polymer,apoly(p-phenylene vinylene) derivative,f unctionalizedw ith p-nitrophenyl esters (PPV-NP) and it inhibits the assembly of amyloid proteins, degrades preformed fibrils,a nd reduces the cytotoxicity of amyloid aggregations in living cells.PPV-NP is attached to the proteins through hydrophobic interactions and irreversible covalent linkage.P PV-NP also exhibited the capacity to eliminate Ab plaques in brain slices in ex vivo assays.T his work represents an innovative attempt to inhibit protein pathogenic aggregates,and may offer insights into the development of therapeutic strategies for amyloidosis.…”

“…[1][2][3][4][5][6][7] On this account, numerous approaches to inhibit amyloid assembly have emerged, ranging from synthetic and natural small-molecule compounds, [4,8,9] peptides, [10,11] antibodies, [12] and nanoparticles [13,14] to artificial chaperones, [15] which make certain achievements to the inhibition of pathogenic aggregates.H owever,t od ate,t he pharmacological treatments for these diseases are still unsatisfactory. [1][2][3][4][5][6][7] On this account, numerous approaches to inhibit amyloid assembly have emerged, ranging from synthetic and natural small-molecule compounds, [4,8,9] peptides, [10,11] antibodies, [12] and nanoparticles [13,14] to artificial chaperones, [15] which make certain achievements to the inhibition of pathogenic aggregates.H owever,t od ate,t he pharmacological treatments for these diseases are still unsatisfactory.…”

“…Inhibition of amyloid assembly is apromising strategy for the treatment of amyloidosis.R eported here is the design and synthesis of areactive conjugated polymer,apoly(p-phenylene vinylene) derivative,f unctionalizedw ith p-nitrophenyl esters (PPV-NP) and it inhibits the assembly of amyloid proteins, degrades preformed fibrils,a nd reduces the cytotoxicity of amyloid aggregations in living cells.PPV-NP is attached to the proteins through hydrophobic interactions and irreversible covalent linkage.P PV-NP also exhibited the capacity to eliminate Ab plaques in brain slices in ex vivo assays.T his work represents an innovative attempt to inhibit protein pathogenic aggregates,and may offer insights into the development of therapeutic strategies for amyloidosis.Proteins are one of the most important basic bio-macromolecules in organisms.T he aberrant assembly of proteins into insoluble amyloid aggregates would disrupt their biological functions and result in the generation of toxic intermediates and amyloidosis,w hich are relevant to ar ange of intractable human disorders such as Alzheimersd isease, Parkinsonsd isease,d ialysis-related amyloidosis,a nd type-2 diabetes. [1][2][3][4][5][6][7] On this account, numerous approaches to inhibit amyloid assembly have emerged, ranging from synthetic and natural small-molecule compounds, [4,8,9] peptides, [10,11] antibodies, [12] and nanoparticles [13,14] to artificial chaperones, [15] which make certain achievements to the inhibition of pathogenic aggregates.H owever,t od ate,t he pharmacological treatments for these diseases are still unsatisfactory. [16] Rational chemical designs to effectively inhibit and disrupt the amyloid assembly are still of great significance.In fact, most previous inhibitors functioned through noncovalent interactions,s uch as hydrophobic interactions, p-p stacking,e lectrostatic interactions,a nd hydrogen bonding.…”