43 results found
Heller GT, Aprile FA, Michaels TCT, et al., 2020, Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease., Sci Adv, Vol: 6
Disordered proteins are challenging therapeutic targets, and no drug is currently in clinical use that modifies the properties of their monomeric states. Here, we identify a small molecule (10074-G5) capable of binding and sequestering the intrinsically disordered amyloid-β (Aβ) peptide in its monomeric, soluble state. Our analysis reveals that this compound interacts with Aβ and inhibits both the primary and secondary nucleation pathways in its aggregation process. We characterize this interaction using biophysical experiments and integrative structural ensemble determination methods. We observe that this molecule increases the conformational entropy of monomeric Aβ while decreasing its hydrophobic surface area. We also show that it rescues a Caenorhabditis elegans model of Aβ-associated toxicity, consistent with the mechanism of action identified from the in silico and in vitro studies. These results illustrate the strategy of stabilizing the monomeric states of disordered proteins with small molecules to alter their behavior for therapeutic purposes.
Ikenoue T, Aprile FA, Sormanni P, et al., 2020, A rationally designed bicyclic peptide remodels Aβ42 aggregation in vitro and reduces its toxicity in a worm model of Alzheimer's disease., Sci Rep, Vol: 10
Bicyclic peptides have great therapeutic potential since they can bridge the gap between small molecules and antibodies by combining a low molecular weight of about 2 kDa with an antibody-like binding specificity. Here we apply a recently developed in silico rational design strategy to produce a bicyclic peptide to target the C-terminal region (residues 31-42) of the 42-residue form of the amyloid β peptide (Aβ42), a protein fragment whose aggregation into amyloid plaques is linked with Alzheimer's disease. We show that this bicyclic peptide is able to remodel the aggregation process of Aβ42 in vitro and to reduce its associated toxicity in vivo in a C. elegans worm model expressing Aβ42. These results provide an initial example of a computational approach to design bicyclic peptides to target specific epitopes on disordered proteins.
Aprile FA, Sormanni P, Podpolny M, et al., 2020, Rational design of a conformation-specific antibody for the quantification of A beta oligomers, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 117, Pages: 13509-13518, ISSN: 0027-8424
Limbocker R, Mannini B, Cataldi R, et al., 2020, Rationally Designed Antibodies as Research Tools to Study the Structure-Toxicity Relationship of Amyloid-beta Oligomers, INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, Vol: 21
Faravelli G, Raimondi S, Marchese L, et al., 2019, C. elegans expressing D76N β2-microglobulin: a model for in vivo screening of drug candidates targeting amyloidosis., Sci Rep, Vol: 9
The availability of a genetic model organism with which to study key molecular events underlying amyloidogenesis is crucial for elucidating the mechanism of the disease and the exploration of new therapeutic avenues. The natural human variant of β2-microglobulin (D76N β2-m) is associated with a fatal familial form of systemic amyloidosis. Hitherto, no animal model has been available for studying in vivo the pathogenicity of this protein. We have established a transgenic C. elegans line, expressing the human D76N β2-m variant. Using the INVertebrate Automated Phenotyping Platform (INVAPP) and the algorithm Paragon, we were able to detect growth and motility impairment in D76N β2-m expressing worms. We also demonstrated the specificity of the β2-m variant in determining the pathological phenotype by rescuing the wild type phenotype when β2-m expression was inhibited by RNA interference (RNAi). Using this model, we have confirmed the efficacy of doxycycline, an inhibitor of the aggregation of amyloidogenic proteins, in rescuing the phenotype. In future, this C. elegans model, in conjunction with the INVAPP/Paragon system, offers the prospect of high-throughput chemical screening in the search for new drug candidates.
Lindstedt PR, Aprile FA, Matos MJ, et al., 2019, Enhancement of the Anti-Aggregation Activity of a Molecular Chaperone Using a Rationally Designed Post-Translational Modification, ACS CENTRAL SCIENCE, Vol: 5, Pages: 1417-1424, ISSN: 2374-7943
De S, Whiten DR, Ruggeri FS, et al., 2019, Soluble aggregates present in cerebrospinal fluid change in size and mechanism of toxicity during Alzheimer's disease progression, ACTA NEUROPATHOLOGICA COMMUNICATIONS, Vol: 7, ISSN: 2051-5960
De S, Wirthensohn DC, Flagmeier P, et al., 2019, Different soluble aggregates of Aβ42 can give rise to cellular toxicity through different mechanisms., Nat Commun, Vol: 10
Protein aggregation is a complex process resulting in the formation of heterogeneous mixtures of aggregate populations that are closely linked to neurodegenerative conditions, such as Alzheimer's disease. Here, we find that soluble aggregates formed at different stages of the aggregation process of amyloid beta (Aβ42) induce the disruption of lipid bilayers and an inflammatory response to different extents. Further, by using gradient ultracentrifugation assay, we show that the smaller aggregates are those most potent at inducing membrane permeability and most effectively inhibited by antibodies binding to the C-terminal region of Aβ42. By contrast, we find that the larger soluble aggregates are those most effective at causing an inflammatory response in microglia cells and more effectively inhibited by antibodies targeting the N-terminal region of Aβ42. These findings suggest that different toxic mechanisms driven by different soluble aggregated species of Aβ42 may contribute to the onset and progression of Alzheimer's disease.
Heller GT, Aprile FA, Bonomi M, et al., 2019, Probing Specificity in Disordered Protein Interactions with Small Molecules using Integrative Methods, 63rd Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 180A-180A, ISSN: 0006-3495
Sormanni P, Aprile FA, Vendruscolo M, 2018, Third generation antibody discovery methods: in silico rational design, CHEMICAL SOCIETY REVIEWS, Vol: 47, Pages: 9137-9157, ISSN: 0306-0012
Perni M, Casford S, Aprile FA, et al., 2018, Automated Behavioral Analysis of Large C. elegans Populations Using a Wide Field-of-view Tracking Platform, JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, ISSN: 1940-087X
Giorgetti S, Greco C, Tortora P, et al., 2018, Targeting Amyloid Aggregation: An Overview of Strategies and Mechanisms, INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, Vol: 19
Giorgetti S, Greco C, Tortora P, et al., 2018, Targeting Amyloid Aggregation: An Overview of Strategies and Mechanisms
<jats:p>Amyloids result from the aggregation of several unrelated proteins, due to either specific mutations or promoting intra- or extra-cellular conditions. Structurally, they are rich in intermolecular &beta;-sheets and are the causative agents of several diseases, both neurodegenerative and systemic. It is believed that the most toxic species are small aggregates, referred to as oligomers, rather than the final fibrillar assemblies. Their mechanisms of toxicity are mostly mediated by aberrant interactions with the cell membranes, with resulting derangement of membrane-related functions. Much effort is being put in the search for natural antiamyloid agents, and/or in the development of synthetic molecules. Actually, it is well documented that the prevention of amyloid aggregation results in several cytoprotective effects. Here, we portray the state of the art in the field. Several natural compounds are effective antiamyloid agents, notably tetracyclines and polyphenols. They are generally non-specific, as documented by their partially overlapping mechanisms, and the capability to interfere with the aggregation of several unrelated proteins. Among rationally designed molecules, we mention the prominent examples of &beta;-breakers peptides, whole antibodies and fragments thereof, and the special case of drugs contrasting transthyretin aggregation. In this framework, we stress the pivotal role of the computational approaches. When combined with biophysical methods, in several cases they have helped clarify in detail the protein/drug modes of interaction, which make it plausible that more effective drugs will be developed in the future.</jats:p>
Perni M, Flagmeier P, Limbocker R, et al., 2018, Multistep Inhibition of alpha-Synuclein Aggregation and Toxicity in Vitro and in Vivo by Trodusquemine, ACS CHEMICAL BIOLOGY, Vol: 13, Pages: 2308-2319, ISSN: 1554-8929
Bongiovanni MN, Aprile FA, Sormanni P, et al., 2018, A Rationally Designed Hsp70 Variant Rescues the Aggregation-Associated Toxicity of Human IAPP in Cultured Pancreatic Islet β-Cells., Int J Mol Sci, Vol: 19
Molecular chaperones are key components of the protein homeostasis system against protein misfolding and aggregation. It has been recently shown that these molecules can be rationally modified to have an enhanced activity against specific amyloidogenic substrates. The resulting molecular chaperone variants can be effective inhibitors of protein aggregation in vitro, thus suggesting that they may provide novel opportunities in biomedical and biotechnological applications. Before such opportunities can be exploited, however, their effects on cell viability should be better characterised. Here, we employ a rational design method to specifically enhance the activity of the 70-kDa heat shock protein (Hsp70) against the aggregation of the human islet amyloid polypeptide (hIAPP, also known as amylin). We then show that the Hsp70 variant that we designed (grafted heat shock protein 70 kDa-human islet amyloid polypeptide, GHsp70-hIAPP) is significantly more effective than the wild type in recovering the viability of cultured pancreatic islet β-cells RIN-m5F upon hIAPP aggregation. These results indicate that a full recovery of the toxic effects of hIAPP aggregates on cultured pancreatic cells can be achieved by increasing the specificity and activity of Hsp70 towards hIAPP, thus providing evidence that the strategy presented here provides a possible route for rationally tailoring molecular chaperones for enhancing their effects in a target-dependent manner.
Bonanomi M, Roffia V, De Palma A, et al., 2018, The polyglutamine protein ataxin-3 enables normal growth under heat shock conditions in the methylotrophic yeast Pichia pastoris (vol 7, 2017), SCIENTIFIC REPORTS, Vol: 8, ISSN: 2045-2322
Perni M, Aprile FA, Casford S, et al., 2017, Delivery of Native Proteins into C-elegans Using a Transduction Protocol Based on Lipid Vesicles, SCIENTIFIC REPORTS, Vol: 7, ISSN: 2045-2322
Bonanomi M, Roffia V, De Palma A, et al., 2017, The polyglutamine protein ataxin-3 enables normal growth under heat shock conditions in the methylotrophic yeast Pichia pastoris, SCIENTIFIC REPORTS, Vol: 7, ISSN: 2045-2322
Bertoldo JB, Rodrigues T, Dunsmore L, et al., 2017, A Water-Bridged Cysteine-Cysteine Redox Regulation Mechanism in Bacterial Protein Tyrosine Phosphatases, CHEM, Vol: 3, Pages: 665-677, ISSN: 2451-9294
Heller GT, Aprilel FA, Bonomi M, et al., 2017, Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide, JOURNAL OF MOLECULAR BIOLOGY, Vol: 429, Pages: 2772-2779, ISSN: 0022-2836
Heller GT, Aprile FA, Vendruscolo M, 2017, Methods of probing the interactions between small molecules and disordered proteins, CELLULAR AND MOLECULAR LIFE SCIENCES, Vol: 74, Pages: 3225-3243, ISSN: 1420-682X
Aprile FA, Kallstig E, Limorenko G, et al., 2017, The molecular chaperones DNAJB6 and Hsp70 cooperate to suppress alpha-synuclein aggregation, SCIENTIFIC REPORTS, Vol: 7, ISSN: 2045-2322
Aprile FA, Sormanni P, Perni M, et al., 2017, Selective targeting of primary and secondary nucleation pathways in A beta 42 aggregation using a rational antibody scanning method, SCIENCE ADVANCES, Vol: 3, ISSN: 2375-2548
Sin O, de Jong T, Mata-Cabana A, et al., 2017, Identification of an RNA Polymerase III Regulator Linked to Disease-Associated Protein Aggregation, MOLECULAR CELL, Vol: 65, Pages: 1096-+, ISSN: 1097-2765
Aprile FA, Arosio P, Fusco G, et al., 2017, Inhibition of alpha-Synuclein Fibril Elongation by Hsp70 Is Governed by a Kinetic Binding Competition between alpha-Synuclein Species, BIOCHEMISTRY, Vol: 56, Pages: 1177-1180, ISSN: 0006-2960
Perni M, Galvagnion C, Maltsev A, et al., 2017, A natural product inhibits the initiation of alpha-synuclein aggregation and suppresses its toxicity, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 114, Pages: E1009-E1017, ISSN: 0027-8424
Borkar AN, Bardaro MF, Camilloni C, et al., 2016, Structure of a low-population binding intermediate in protein-RNA recognition, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 113, Pages: 7171-7176, ISSN: 0027-8424
Arosio P, Hu K, Aprile FA, et al., 2016, Microfluidic Diffusion Viscometer for Rapid Analysis of Complex Solutions, ANALYTICAL CHEMISTRY, Vol: 88, Pages: 3488-3493, ISSN: 0003-2700
Arosio P, Mueller T, Rajah L, et al., 2016, Microfluidic Diffusion Analysis of the Sizes and Interactions of Proteins under Native Solution Conditions, ACS NANO, Vol: 10, Pages: 333-341, ISSN: 1936-0851
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