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Dong Q, Cui Z, Wu X, Li L, Lu F, Liu F. Natural flavonoid hesperetin blocks amyloid β-protein fibrillogenesis, depolymerizes preformed fibrils and alleviates cytotoxicity caused by amyloids. Food Funct 2024; 15:4233-4245. [PMID: 38517352 DOI: 10.1039/d3fo05566c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
The aggregation of β-amyloid (Aβ) peptides to form amyloid plaques is one of the primary hallmarks for Alzheimer's disease (AD). Dietary flavonoid supplements containing hesperetin have an ability to decline the risk of developing AD, but the molecular mechanism is still unclear. In this work, hesperetin, a flavanone abundant in citrus fruits, has been proven to prevent the formation of Aβ aggregates and depolymerized preformed fibrils in a concentration-dependent fashion. Hesperetin inhibited the conformational conversion from the natural structure to a β-sheet-rich conformation. It was found that hesperetin significantly reduced the cytotoxicity and relieved oxidative stress eventuated by Aβ aggregates in a concentration-dependent manner. Additionally, the beneficial effects of hesperetin were confirmed in Caenorhabditis elegans, including the inhibition of the formation and deposition of Aβ aggregates and extension of their lifespan. Finally, the results of molecular dynamics simulations showed that hesperetin directly interacted with an Aβ42 pentamer mainly through strong non-polar and electrostatic interactions, which destroyed the structural stability of the preformed pentamer. To summarize, hesperetin exhibits great potential as a prospective dietary supplement for preventing and improving AD.
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Affiliation(s)
- Qinchen Dong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China.
| | - Zhan Cui
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China.
| | - Xinming Wu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China.
| | - Li Li
- College of Sciences, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China.
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin, 300457, P. R. China
- Tianjin Key Laboratory of Industrial Microbiology, Tianjin, 300457, P. R. China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China.
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Leguizamon Herrera VL, Buell AK, Willbold D, Barz B. Interaction of Therapeutic d-Peptides with Aβ42 Monomers, Thermodynamics, and Binding Analysis. ACS Chem Neurosci 2022; 13:1638-1650. [PMID: 35580288 DOI: 10.1021/acschemneuro.2c00102] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The aggregation of the amyloid-β (Aβ) peptide is a major hallmark of Alzheimer's disease. This peptide can aggregate into oligomers, proto-fibrils, and mature fibrils, which eventually assemble into amyloid plaques. The peptide monomers are the smallest assembly units and play an important role in most of the individual processes involved in amyloid fibril formation, such as primary and secondary nucleation and elongation. Several d-peptides have been confirmed as promising candidates to inhibit the aggregation of Aβ into toxic oligomers and fibrils by specifically interacting with monomeric species. In this work, we elucidate the structural interaction and thermodynamics of binding between three d-peptides (D3, ANK6, and RD2) and Aβ42 monomers by means of enhanced molecular dynamics simulations. Our study derives thermodynamic energies in good agreement with experimental values and suggests that there is an enhanced binding for D3 and ANK6, which leads to more stable complexes than for RD2. The binding of D3 to Aβ42 is shown to be weakly exothermic and mainly entropically driven, whereas the complex formation between the ANK6 and RD2 with the Aβ42 free monomer is weakly endothermic. In addition, the changes in the solvent-accessible surface area and the radius of gyration support that the binding between Aβ42 and d-peptides is mainly driven by electrostatic and hydrophobic interactions and leads to more compact conformations.
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Affiliation(s)
| | - Alexander K. Buell
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Dieter Willbold
- Institute of Biological Information Processing-Structural Biochemistry (IBI-7), Research Centre Jülich, 52425 Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Bogdan Barz
- Institute of Biological Information Processing-Structural Biochemistry (IBI-7), Research Centre Jülich, 52425 Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
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Chakraborty S, Das P. Emergence of Alternative Structures in Amyloid Beta 1-42 Monomeric Landscape by N-terminal Hexapeptide Amyloid Inhibitors. Sci Rep 2017; 7:9941. [PMID: 28855598 PMCID: PMC5577341 DOI: 10.1038/s41598-017-10212-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/04/2017] [Indexed: 02/01/2023] Open
Abstract
Alzheimer’s disease (AD) is characterized by deposition of amyloid beta (Aβ) peptides into senile plaques in the brain. While most familial mutations are associated with early-onset AD, recent studies report the AD-protective nature of two genetic human Aβ variants, i.e. A2T and A2V, in the heterozygous state. The mixture of A2V Aβ1-6 (Aβ6) hexapeptide and WT Aβ1–42 (Αβ42) is also found neuroprotective. Motivated by these findings, in this study we investigate the effects of WT, A2V, and A2T Aβ6 hexapeptide binding on the monomeric WT Aβ42 landscape. For this purpose, we have performed extensive atomistic Replica Exchange Molecular Dynamics simulations, elucidating preferential binding of Aβ42 with the A2V and A2T hexapeptides compared to WT Aβ6. A notable reorganization of the Aβ42 landscape is revealed due to hexapeptide association, as manifested by lowering of transient interactions between the central and C-terminal hydrophobic patches. Concurrently, Aβ6-bound Aβ42 monomer exhibits alternative structural features that are strongly dependent on the hexapeptide sequence. For example, a central helix is more frequently populated within the A2T-bound monomer, while A2V-bound Aβ42 is often enhanced in overall disorder. Taken together, the present simulations offer novel molecular insights onto the effect of the N-terminal hexapeptide binding on the Aβ42 monomer structure, which might help in explaining their reported amyloid inhibition properties.
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Affiliation(s)
| | - Payel Das
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY, 10598, USA.
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4
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Das P, Chacko AR, Belfort G. Alzheimer's Protective Cross-Interaction between Wild-Type and A2T Variants Alters Aβ 42 Dimer Structure. ACS Chem Neurosci 2017; 8:606-618. [PMID: 28292185 DOI: 10.1021/acschemneuro.6b00357] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Whole genome sequencing has recently revealed the protective effect of a single A2T mutation in heterozygous carriers against Alzheimer's disease (AD) and age-related cognitive decline. The impact of the protective cross-interaction between the wild-type (WT) and A2T variants on the dimer structure is therefore of high interest, as the Aβ dimers are the smallest known neurotoxic species. Toward this goal, extensive atomistic replica exchange molecular dynamics simulations of the solvated WT homo- and A2T hetero- Aβ1-42 dimers have been performed, resulting into a total of 51 μs of sampling for each system. Weakening of a set of transient, intrachain contacts formed between the central and C-terminal hydrophobic residues is observed in the heterodimeric system. The majority of the heterodimers with reduced interaction between central and C-terminal regions lack any significant secondary structure and display a weak interchain interface. Interestingly, the A2T N-terminus, particularly residue F4, is frequently engaged in tertiary and quaternary interactions with central and C-terminal hydrophobic residues in those distinct structures, leading to hydrophobic burial. This atypical involvement of the N-terminus within A2T heterodimer revealed in our simulations implies possible interference on Aβ42 aggregation and toxic oligomer formation, which is consistent with experiments. In conclusion, the present study provides detailed structural insights onto A2T Aβ42 heterodimer, which might provide molecular insights onto the AD protective effect of the A2T mutation in the heterozygous state.
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Affiliation(s)
- Payel Das
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Anita R. Chacko
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Georges Belfort
- Howard
P. Isermann Department of Chemical and Biological Engineering, and
Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180-3590, United States
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5
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Das P, Murray B, Belfort G. Alzheimer's protective A2T mutation changes the conformational landscape of the Aβ₁₋₄₂ monomer differently than does the A2V mutation. Biophys J 2015; 108:738-47. [PMID: 25650940 DOI: 10.1016/j.bpj.2014.12.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/01/2014] [Accepted: 12/04/2014] [Indexed: 12/20/2022] Open
Abstract
The aggregation of amyloid-β (Aβ) peptides plays a crucial role in the etiology of Alzheimer's disease (AD). Recently, it has been reported that an A2T mutation in Aβ can protect against AD. Interestingly, a nonpolar A2V mutation also has been found to offer protection against AD in the heterozygous state, although it causes early-onset AD in homozygous carriers. Since the conformational landscape of the Aβ monomer is known to directly contribute to the early-stage aggregation mechanism, it is important to characterize the effects of the A2T and A2V mutations on Aβ₁₋₄₂ monomer structure. Here, we have performed extensive atomistic replica-exchange molecular dynamics simulations of the solvated wild-type (WT), A2V, and A2T Aβ₁₋₄₂ monomers. Our simulations reveal that although all three variants remain as collapsed coils in solution, there exist significant structural differences among them at shorter timescales. A2V exhibits an enhanced double-hairpin population in comparison to the WT, similar to those reported in toxic WT Aβ₁₋₄₂ oligomers. Such double-hairpin formation is caused by hydrophobic clustering between the N-terminus and the central and C-terminal hydrophobic patches. In contrast, the A2T mutation causes the N-terminus to engage in unusual electrostatic interactions with distant residues, such as K16 and E22, resulting in a unique population comprising only the C-terminal hairpin. These findings imply that a single A2X (where X = V or T) mutation in the primarily disordered N-terminus of the Aβ₁₋₄₂ monomer can dramatically alter the β-hairpin population and switch the equilibrium toward alternative structures. The atomistically detailed, comparative view of the structural landscapes of A2V and A2T variant monomers obtained in this study can enhance our understanding of the mechanistic differences in their early-stage aggregation.
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Affiliation(s)
- Payel Das
- Soft Matter Theory and Simulations Group, Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York.
| | - Brian Murray
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Georges Belfort
- Howard P. Isermann Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
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Hernández-Rodríguez M, Correa-Basurto J, Nicolás-Vázquez MI, Miranda-Ruvalcaba R, Benítez-Cardoza CG, Reséndiz-Albor AA, Méndez-Méndez JV, Rosales-Hernández MC. Virtual and In Vitro Screens Reveal a Potential Pharmacophore that Avoids the Fibrillization of Aβ1-42. PLoS One 2015; 10:e0130263. [PMID: 26172152 PMCID: PMC4501547 DOI: 10.1371/journal.pone.0130263] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 05/18/2015] [Indexed: 11/25/2022] Open
Abstract
Among the multiple factors that induce Alzheimer’s disease, aggregation of the amyloid β peptide (Aβ) is considered the most important due to the ability of the 42-amino acid Aβ peptides (Aβ1–42) to form oligomers and fibrils, which constitute Aβ pathological aggregates. For this reason, the development of inhibitors of Aβ1–42 pathological aggregation represents a field of research interest. Several Aβ1–42 fibrillization inhibitors possess tertiary amine and aromatic moieties. In the present study, we selected 26 compounds containing tertiary amine and aromatic moieties with or without substituents and performed theoretical studies that allowed us to select four compounds according to their free energy values for Aβ1–42 in α-helix (Aβ-α), random coil (Aβ-RC) and β-sheet (Aβ-β) conformations. Docking studies revealed that compound 5 had a higher affinity for Aβ-α and Aβ-RC than the other compounds. In vitro, this compound was able to abolish Thioflavin T fluorescence and favored an RC conformation of Aβ1–42 in circular dichroism studies, resulting in the formation of amorphous aggregates as shown by atomic force microscopy. The results obtained from quantum studies allowed us to identify a possible pharmacophore that can be used to design Aβ1–42 aggregation inhibitors. In conclusion, compounds with higher affinity for Aβ-α and Aβ-RC prevented the formation of oligomeric species.
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Affiliation(s)
- Maricarmen Hernández-Rodríguez
- Laboratorio de Modelado Molecular y Diseño de Fármacos, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón S/N, Delegación Miguel Hidalgo, México D.F., México
- Laboratorio de Biofísica y Biocatálisis, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón S/N, Delegación Miguel Hidalgo, México D.F., México
| | - José Correa-Basurto
- Laboratorio de Modelado Molecular y Diseño de Fármacos, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón S/N, Delegación Miguel Hidalgo, México D.F., México
- * E-mail: (MCRH): (JCB)
| | - María Inés Nicolás-Vázquez
- Quimica inorgánica-orgánica del Departamento de Ciencias Químicas, de la Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo S/N, Santa María las Torres, Cuautitlán Izcalli, Estado de México, México
| | - René Miranda-Ruvalcaba
- Quimica inorgánica-orgánica del Departamento de Ciencias Químicas, de la Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo S/N, Santa María las Torres, Cuautitlán Izcalli, Estado de México, México
| | - Claudia Guadalupe Benítez-Cardoza
- Laboratorio de Investigación Bioquímica, Sección de Estudios de Posgrado e Investigación, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Guillermo Massieu H 239, Gustavo A. Madero, La Escalera, México D.F., México
| | - Aldo Arturo Reséndiz-Albor
- Laboratorio de Investigación en Inmunología., Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón S/N, Delegación Miguel Hidalgo, México D.F., México
| | - Juan Vicente Méndez-Méndez
- Centro de Nanociencias y Micro y Nanotecnología, Instituto Politécnico Nacional, Luis Enrique Erro S/N, U. Prof Adolfo López Mateos, Gustavo A. Madero, México D.F., México
| | - Martha C. Rosales-Hernández
- Laboratorio de Biofísica y Biocatálisis, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón S/N, Delegación Miguel Hidalgo, México D.F., México
- * E-mail: (MCRH): (JCB)
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7
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Li G, Pomès R. Binding mechanism of inositol stereoisomers to monomers and aggregates of Aβ(16-22). J Phys Chem B 2013; 117:6603-13. [PMID: 23627280 DOI: 10.1021/jp311350r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Alzheimer's disease (AD) is a severe neurodegenerative disease with no cure. A potential therapeutic approach is to prevent or reverse the amyloid formation of Aβ42, a key pathological hallmark of AD. We examine the molecular basis for stereochemistry-dependent inhibition of the formation of Aβ fibrils in vitro by a polyol, scyllo-inositol. We present molecular dynamics simulations of the monomeric, disordered aggregate, and protofibrillar states of Aβ(16-22), an amyloid-forming peptide fragment of full-length Aβ, successively with and without scyllo-inositol and its inactive stereoisomer chiro-inositol. Both stereoisomers bind monomers and disordered aggregates with similar affinities of 10-120 mM, whereas binding to β-sheet-containing protofibrils yields affinities of 0.2-0.5 mM commensurate with in vitro inhibitory concentrations of scyllo-inositol. Moreover, scyllo-inositol displays a higher binding specificity for phenylalanine-lined grooves on the protofibril surface, suggesting that scyllo-inositol coats the surface of Aβ protofibrils and disrupts their lateral stacking into amyloid fibrils.
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Affiliation(s)
- Grace Li
- Department of Biochemistry, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1
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8
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Desbène C, Malaplate-Armand C, Youssef I, Garcia P, Stenger C, Sauvée M, Fischer N, Rimet D, Koziel V, Escanyé MC, Oster T, Kriem B, Yen FT, Pillot T, Olivier JL. Critical role of cPLA2 in Aβ oligomer-induced neurodegeneration and memory deficit. Neurobiol Aging 2011; 33:1123.e17-29. [PMID: 22188721 DOI: 10.1016/j.neurobiolaging.2011.11.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 11/03/2011] [Accepted: 11/04/2011] [Indexed: 12/23/2022]
Abstract
Soluble beta-amyloid (Aβ) oligomers are considered to putatively play a critical role in the early synapse loss and cognitive impairment observed in Alzheimer's disease. We previously demonstrated that Aβ oligomers activate cytosolic phospholipase A(2) (cPLA(2)), which specifically releases arachidonic acid from membrane phospholipids. We here observed that cPLA(2) gene inactivation prevented the alterations of cognitive abilities and the reduction of hippocampal synaptic markers levels noticed upon a single intracerebroventricular injection of Aβ oligomers in wild type mice. We further demonstrated that the Aβ oligomer-induced sphingomyelinase activation was suppressed and that phosphorylation of Akt/protein kinase B (PKB) was preserved in neuronal cells isolated from cPLA(2)(-/-) mice. Interestingly, expression of the Aβ precursor protein (APP) was reduced in hippocampus homogenates and neuronal cells from cPLA(2)(-/-) mice, but the relationship with the resistance of these mice to the Aβ oligomer toxicity requires further investigation. These results therefore show that cPLA(2) plays a key role in the Aβ oligomer-associated neurodegeneration, and as such represents a potential therapeutic target for the treatment of Alzheimer's disease.
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Affiliation(s)
- Cédric Desbène
- Lipidomix (EA 4422), INPL-ENSAIA, Université de Lorraine, Vandœuvre-lès-Nancy, France
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9
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Frydman-Marom A, Shaltiel-Karyo R, Moshe S, Gazit E. The generic amyloid formation inhibition effect of a designed small aromatic β-breaking peptide. Amyloid 2011; 18:119-27. [PMID: 21651439 DOI: 10.3109/13506129.2011.582902] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The development of generic inhibitors in order to control the formation of amyloid fibrils and early oligomers is still an unmet medical need. As it is hypothesized that amyloid assemblies represent a generic protein supramolecular structure of low free energy, targeting the key molecular recognition and self-assembly events may provide the route for the development of such potential therapeutic agents. We have previously demonstrated the ability of hybrid molecules composed of an aromatic moiety and the α-aminoisobutyric acid β-sheet breaker elements to act as excellent inhibitors of amyloid fibril formation. Specifically, the D-Trp-Aib was shown to be a superb inhibitor of the formation of Alzheimer's disease β-amyloid fibrils and oligomers both in vitro and in vivo. Here, we demonstrate that the rationally designed molecule has the generic ability to inhibit amyloid fibril formation by calcitonin, α-synuclein, and the islet amyloid polypeptide. Moreover, we demonstrate the inability of two modified peptides, D-Ala-Aib and D-Trp-Ala, to inhibit and disassemble amyloid fibril formation, a fact that provides an additional evidence for the suggested structural basis of the inhibitor activity. Taken together, we believe that the use of β-breaker elements combined with aromatic moiety may present a promising approach for the development of fibrillization inhibition drug candidate.
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Affiliation(s)
- Anat Frydman-Marom
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
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10
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Ozawa D, Kaji Y, Yagi H, Sakurai K, Kawakami T, Naiki H, Goto Y. Destruction of amyloid fibrils of keratoepithelin peptides by laser irradiation coupled with amyloid-specific thioflavin T. J Biol Chem 2011; 286:10856-63. [PMID: 21300800 DOI: 10.1074/jbc.m111.222901] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Mutations in keratoepithelin are associated with blinding ocular diseases, including lattice corneal dystrophy type 1 and granular corneal dystrophy type 2. These diseases are characterized by deposits of amyloid fibrils and/or granular non-amyloid aggregates in the cornea. Removing the deposits in the cornea is important for treatment. Previously, we reported the destruction of amyloid fibrils of β(2)-microglobulin K3 fragments and amyloid β by laser irradiation coupled with the binding of an amyloid-specific thioflavin T. Here, we studied the effects of this combination on the amyloid fibrils of two 22-residue fragments of keratoepithelin. The direct observation of individual amyloid fibrils was performed in real time using total internal reflection fluorescence microscopy. Both types of amyloid fibrils were broken up by the laser irradiation, dependent on the laser power. The results suggest the laser-induced destruction of amyloid fibrils to be a useful strategy for the treatment of these corneal dystrophies.
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Affiliation(s)
- Daisaku Ozawa
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
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11
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Colombo G, Margosio B, Ragona L, Neves M, Bonifacio S, Annis DS, Stravalaci M, Tomaselli S, Giavazzi R, Rusnati M, Presta M, Zetta L, Mosher DF, Ribatti D, Gobbi M, Taraboletti G. Non-peptidic thrombospondin-1 mimics as fibroblast growth factor-2 inhibitors: an integrated strategy for the development of new antiangiogenic compounds. J Biol Chem 2010; 285:8733-42. [PMID: 20056600 DOI: 10.1074/jbc.m109.085605] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Endogenous inhibitors of angiogenesis, such as thrombospondin-1 (TSP-1), are promising sources of therapeutic agents to treat angiogenesis-driven diseases, including cancer. TSP-1 regulates angiogenesis through different mechanisms, including binding and sequestration of the angiogenic factor fibroblast growth factor-2 (FGF-2), through a site located in the calcium binding type III repeats. We hypothesized that the FGF-2 binding sequence of TSP-1 might serve as a template for the development of inhibitors of angiogenesis. Using a peptide array approach followed by binding assays with synthetic peptides and recombinant proteins, we identified a FGF-2 binding sequence of TSP-1 in the 15-mer sequence DDDDDNDKIPDDRDN. Molecular dynamics simulations, taking the full flexibility of the ligand and receptor into account, and nuclear magnetic resonance identified the relevant residues and conformational determinants for the peptide-FGF interaction. This information was translated into a pharmacophore model used to screen the NCI2003 small molecule databases, leading to the identification of three small molecules that bound FGF-2 with affinity in the submicromolar range. The lead compounds inhibited FGF-2-induced endothelial cell proliferation in vitro and affected angiogenesis induced by FGF-2 in the chicken chorioallantoic membrane assay. These small molecules, therefore, represent promising leads for the development of antiangiogenic agents. Altogether, this study demonstrates that new biological insights obtained by integrated multidisciplinary approaches can be used to develop small molecule mimics of endogenous proteins as therapeutic agents.
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Affiliation(s)
- Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milan 20131, Italy
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12
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Li H, Luo Y, Derreumaux P, Wei G. Effects of the RGTFEGKF Inhibitor on the Structures of the Transmembrane Fragment 70−86 of Glycophorin A: An All-Atom Molecular Dynamics Study. J Phys Chem B 2009; 114:1004-9. [DOI: 10.1021/jp908889q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Huiyu Li
- Surface Physics Laboratory (National Key Laboratory) and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, People’s Republic of China and Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico−Chimique et Université Paris Diderot, Paris 7,13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Yin Luo
- Surface Physics Laboratory (National Key Laboratory) and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, People’s Republic of China and Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico−Chimique et Université Paris Diderot, Paris 7,13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Surface Physics Laboratory (National Key Laboratory) and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, People’s Republic of China and Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico−Chimique et Université Paris Diderot, Paris 7,13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Guanghong Wei
- Surface Physics Laboratory (National Key Laboratory) and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, People’s Republic of China and Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico−Chimique et Université Paris Diderot, Paris 7,13 rue Pierre et Marie Curie, 75005 Paris, France
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13
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Kranjc A, Bongarzone S, Rossetti G, Biarnés X, Cavalli A, Bolognesi ML, Roberti M, Legname G, Carloni P. Docking Ligands on Protein Surfaces: The Case Study of Prion Protein. J Chem Theory Comput 2009; 5:2565-73. [PMID: 26616631 DOI: 10.1021/ct900257t] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular docking of ligands targeting proteins undergoing fibrillization in neurodegenerative diseases is difficult because of the lack of deep binding sites. Here we extend standard docking methods with free energy simulations in explicit solvent to address this issue in the context of the prion protein surface. We focus on a specific ligand (2-pyrrolidin-1-yl-N-[4-[4-(2-pyrrolidin-1-yl-acetylamino)-benzyl]-phenyl]-acetamide), which binds to the structured part of the protein as shown by NMR (Kuwata, K. et al. Proc Natl Acad Sci U.S.A. 2007, 104, 11921-11926). The calculated free energy of dissociation (7.8 ± 0.9 kcal/mol) is in good agreement with the value derived by the experimental dissociation constant (Kd = 3.9 μM, corresponding to ΔG(0) = -7.5 kcal/mol). Several binding poses are predicted, including the one reported previously. Our prediction is fully consistent with the presence of multiple binding sites, emerging from NMR measurements. Our molecular simulation-based approach emerges, therefore, as a useful tool to predict poses and affinities of ligand binding to protein surfaces.
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Affiliation(s)
- Agata Kranjc
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
| | - Salvatore Bongarzone
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
| | - Giulia Rossetti
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
| | - Xevi Biarnés
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
| | - Andrea Cavalli
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
| | - Maria Laura Bolognesi
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
| | - Marinella Roberti
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
| | - Giuseppe Legname
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
| | - Paolo Carloni
- Statistical and Biological Physics Sector, Neurobiology Sector, International School for Advanced Studies (SISSA), SISSA-Unit, Italian Institute of Technology, 34014 Trieste, Italy, Department of Pharmaceutical Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy, Department of Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy, and CNR-INFM-DEMOCRITOS Modeling Center for Research in Atomistic Simulation, 34014 Trieste, Italy
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