Rational design of potent domain antibody inhibitors of amyloid fibril assembly

Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 11/2012; 110(4). DOI: 10.1073/pnas.1208797109
Source: PubMed


Antibodies hold significant potential for inhibiting toxic protein aggregation associated with conformational disorders such as Alzheimer's and Huntington's diseases. However, near-stoichiometric antibody concentrations are typically required to completely inhibit protein aggregation. We posited that the molecular interactions mediating amyloid fibril formation could be harnessed to generate antibodies with potent antiaggregation. Here we report that grafting small amyloidogenic peptides (6-10 residues) into the complementarity-determining regions of a single-domain (V(H)) antibody yields potent domain antibody inhibitors of amyloid formation. Grafted AMyloid-Motif AntiBODIES (gammabodies) presenting hydrophobic peptides from Aβ (Alzheimer's disease), α-Synuclein (Parkinson's disease), and islet amyloid polypeptide (type 2 diabetes) inhibit fibril assembly of each corresponding polypeptide at low substoichiometric concentrations (1:10 gammabody:monomer molar ratio). In contrast, sequence- and conformation-specific antibodies that were obtained via immunization are unable to prevent fibrillization at the same substoichiometric concentrations. Gammabodies prevent amyloid formation by converting monomers and/or fibrillar intermediates into small complexes that are unstructured and benign. We expect that our antibody design approach-which eliminates the need for immunization or screening to identify sequence-specific domain antibody inhibitors-can be readily extended to generate potent aggregation inhibitors of other amyloidogenic polypeptides linked to human disease.

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    • "Conversely, the specificity of aggregationdetermining interactions can also be used to inhibit aggregation [16] [17]. Similarly, grafting the aggregationprone sequence of Aβ, α-synuclein or IAPP in place of the complementarity-determining region loop of a single domain antibody leads to the specific binding of these antibodies to their respective target protein thereby inhibiting its aggregation [18]. "
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    ABSTRACT: Protein aggregation is sequence specific, favoring self-assembly over cross-seeding with non-homologous sequences. Still, as the majority of proteins in a proteome are aggregation prone, the high level of homogeneity of protein inclusions in vivo both during recombinant overexpression and in disease remains surprising. To investigate the selectivity of protein aggregation in a proteomic context, we here compared the selectivity of aggregation-determined interactions with antibody binding. To that purpose, we synthesized biotin-labeled peptides, corresponding to aggregation-determining sequences of the bacterial protein β-galactosidase and two human disease biomarkers: C-reactive protein and prostate-specific antigen. We analyzed the selectivity of their interactions in Escherichia coli lysate, human serum and human seminal plasma, respectively, using a Western blot-like approach in which the aggregating peptides replace the conventional antibody. We observed specific peptide accumulation in the same bands detected by antibody staining. Combined spectroscopic and mutagenic studies confirmed accumulation resulted from binding of the peptide on the identical sequence of the immobilized target protein. Further, we analyzed the sequence redundancy of aggregating sequences and found that about 90% of them are unique within their proteome. As a result, the combined specificity and low sequence redundancy of aggregating sequences therefore contribute to the observed homogeneity of protein aggregation in vivo. This suggests that these intrinsic proteomic properties naturally compartmentalize aggregation events in sequence space. In the event of physiological stress, this might benefit the ability of cells to respond to proteostatic stress by allowing chaperones to focus on specific aggregation events rather than having to face systemic proteostatic failure.
    Full-text · Article · Nov 2014 · Journal of Molecular Biology
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    • "Since the amyloid fibrils from different sources display common characteristics, several groups have developed antibodies capable of recognizing the so-called ‘universal amyloid epitope’ [8]–[11]. All of these antibodies are able to distinguish between the mature amyloid structure and the monomeric or oligomeric intermediate precursors of amyloid aggregation [8]–[10]. "
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    ABSTRACT: Amyloid fibrils are associated with many maladies, including Alzheimer's disease (AD). The isolation of amyloids from natural materials is very challenging because the extreme structural stability of amyloid fibrils makes it difficult to apply conventional protein science protocols to their purification. A protocol to isolate and detect amyloids is desired for the diagnosis of amyloid diseases and for the identification of new functional amyloids. Our aim was to develop a protocol to purify amyloid from organisms, based on the particular characteristics of the amyloid fold, such as its resistance to proteolysis and its capacity to be recognized by specific conformational antibodies. We used a two-step strategy with proteolytic digestion as the first step followed by immunoprecipitation using the amyloid conformational antibody LOC. We tested the efficacy of this method using as models amyloid fibrils produced in vitro, tissue extracts from C. elegans that overexpress Aβ peptide, and cerebrospinal fluid (CSF) from patients diagnosed with AD. We were able to immunoprecipitate Aβ1-40 amyloid fibrils, produced in vitro and then added to complex biological extracts, but not α-synuclein and gelsolin fibrils. This method was useful for isolating amyloid fibrils from tissue homogenates from a C. elegans AD model, especially from aged worms. Although we were able to capture picogram quantities of Aβ1-40 amyloid fibrils produced in vitro when added to complex biological solutions, we could not detect any Aβ amyloid aggregates in CSF from AD patients. Our results show that although immunoprecipitation using the LOC antibody is useful for isolating Aβ1-40 amyloid fibrils, it fails to capture fibrils of other amyloidogenic proteins, such as α-synuclein and gelsolin. Additional research might be needed to improve the affinity of these amyloid conformational antibodies for an array of amyloid fibrils without compromising their selectivity before application of this protocol to the isolation of amyloids.
    Full-text · Article · Aug 2014 · PLoS ONE
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    • "/100kE/100lD (DED-Aβ12–21-DED) @BULLET97D/98E/99D (DED-Aβ12–21) @BULLET100gD/100hE/100iD (Aβ12–21-DED) @BULLET97D/98E/99D/100jD/100kE/100lD (DED-Aβ18–27-DED) @BULLET97D/98E/99D (DED-Aβ18–27) @BULLET100gD/100hE/100iD (Aβ18–27-DED) [92] [98] Aβ18 "
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    ABSTRACT: Monoclonal antibodies are a remarkably successful class of therapeutics used to treat a wide range of indications. There has been growing interest in smaller antibody fragments such as Fabs, scFvs and domain antibodies in recent years. In particular, the development of human VH and VL single-domain antibody therapeutics, as stand-alone affinity reagents or as "warheads" for larger molecules, are favored over other sources of antibodies due to their perceived lack of immunogenicity in humans. However, unlike camelid heavy-chain antibody variable domains (VHHs) which almost unanimously resist aggregation and are highly stable, human VHs and VLs are prone to aggregation and exhibit poor solubility. Approaches to reduce VH and VL aggregation and increase solubility are therefore very active areas of research within the antibody engineering community. Here we extensively chronicle the various mutational approaches that have been applied to human VHs and VLs to improve their biophysical properties such as expression yield, thermal stability, reversible unfolding and aggregation resistance. In addition, we describe stages of the VH and VL development process where these mutations could best be implemented. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody. Guest Editors: Kouhei Tsumoto, Yoshihisa Hagihara and Dirk Saerens.
    Full-text · Article · Jul 2014 · Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics
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