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Kaur A, Goyal D, Goyal B. An α-helix mimetic oligopyridylamide, ADH-31, modulates Aβ 42 monomer aggregation and destabilizes protofibril structures: insights from molecular dynamics simulations. Phys Chem Chem Phys 2020; 22:28055-28073. [PMID: 33289734 DOI: 10.1039/d0cp04672h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Alzheimer's disease (AD), an epidemic growing worldwide due to no effective medical aid available in the market, is a neurological disorder. AD is known to be directly associated with the toxicity of amyloid-β (Aβ) aggregates. In search of potent inhibitors of Aβ aggregation, Hamilton and co-workers reported an α-helix mimetic, ADH-31, which acts as a powerful antagonist of Aβ42 aggregation. To identify the key interactions between protein-ligand complexes and to gain insights into the inhibitory mechanism of ADH-31 against Aβ42 aggregation, molecular dynamics (MD) simulations were performed in the present study. The MD simulations highlighted that ADH-31 showed distinct binding capabilities with residues spanning from the N-terminal to the central hydrophobic core (CHC) region of Aβ42 and restricted the conformational transition of the helix-rich structure of Aβ42 into another form of secondary structures (coil/turn/β-sheet). Hydrophobic contacts, hydrogen bonding and π-π interaction contribute to the strong binding between ADH-31 and Aβ42 monomer. The Dictionary of Secondary Structure of Proteins (DSSP) analysis highlighted that the probability of helical content increases from 38.5% to 50.2% and the turn content reduces from 14.7% to 6.2% with almost complete loss of the β-sheet structure (4.5% to 0%) in the Aβ42 monomer + ADH-31 complex. The per-residue binding free energy analysis demonstrated that Arg5, Tyr10, His14, Gln15, Lys16, Val18, Phe19 and Lys28 residues of Aβ42 are responsible for the favourable binding free energy in Aβ42 monomer + ADH-31 complex, which is consistent with the 2D HSQC NMR of the Aβ42 monomer that depicted a change in the chemical shift of residues spanning from Glu11 to Phe20 in the presence of ADH-31. The MD simulations highlighted the prevention of sampling of amyloidogenic β-strand conformations in Aβ42 trimer in the presence of ADH-31 as well as the ability of ADH-31 to destabilize Aβ42 trimer and protofibril structures. The lower binding affinity between Aβ42 trimer chains in the presence of ADH-31 highlights the destabilization of the Aβ42 trimer structure. Overall, MD results highlighted that ADH-31 inhibited Aβ42 aggregation by constraining Aβ peptides into helical conformation and destabilized Aβ42 trimer as well as protofibril structures. The present study provides a theoretical insight into the atomic level details of the inhibitory mechanism of ADH-31 against Aβ42 aggregation as well as protofibril destabilization and could be implemented in the structure-based drug design of potent therapeutic agents for AD.
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Affiliation(s)
- Anupamjeet Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India.
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De D, Bhattacharjee P, Das H, Kumar KS, Biswas SC, Bhattacharyya D. Destabilization of β-amyloid aggregates by thrombin derived peptide: plausible role of thrombin in neuroprotection. FEBS J 2020; 287:2386-2413. [PMID: 31747135 DOI: 10.1111/febs.15149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 09/04/2019] [Accepted: 11/19/2019] [Indexed: 01/06/2023]
Abstract
β-amyloid (Aβ) aggregates involved in Alzheimer's disease (AD) are resistant to proteases but could be destabilized by small peptides designed to target specific hydrophobic regions of Aβ that take part in aggregate assembly. Since thrombin and AD are intricately connected, and elastase modulates thrombin activity, elastase-digested thrombin peptides were verified for intervention in the Aβ-aggregation pathway. Intact or elastase-digested thrombin destabilized Aβ fibril, as demonstrated by thioflavin T assay. Peptides were synthesized employing thrombin as a template, of which, a hexapeptide (T3) showed maximum destabilization at 1 µm. ExPASy peptide cutter software coupled with mass spectrometric analysis confirmed the generation of T3 peptide from elastase-digested thrombin. TEM micrographs revealed that 30-day incubation of preformed Aβ fibrils or monomers with T3 resulted in destabilization or inhibition, respectively, leading mostly to particles of 1.74 ± 0.17 nm, which roughly corresponded to Aβ monomer. Surface plasmon resonance employing CM5 chip coupled with Aβ40 mouse monoclonal antibody showed a drop in response when T3 was incubated with Aβ fibrils between 2 and 8 h. 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide and confocal microscopy demonstrated the ability of T3 to rescue neuroblastoma cells from Aβ oligomer-induced cytotoxic damage. Although no [Aβ-T3] adduct could be detected by mass spectrometry, an initial interaction appeared to facilitate the process of destabilization/inhibition of aggregation. T3 was comparable to standard β-sheet breaker peptides, LPFFD and KLVFF in terms of Aβ aggregate destabilization. High hydrophobicity values coupled with recognition and breaking elements make T3 a potential candidate for future therapeutic applications.
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Affiliation(s)
- Debashree De
- Division of Structural Biology and Bioinformatics, CSIR - Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Payel Bhattacharjee
- Division of Structural Biology and Bioinformatics, CSIR - Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Hrishita Das
- Division of Cell Biology and Physiology, CSIR - Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Karri Suresh Kumar
- Central Instrument Facility, CSIR - Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Subhas Chandra Biswas
- Division of Cell Biology and Physiology, CSIR - Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Debasish Bhattacharyya
- Division of Structural Biology and Bioinformatics, CSIR - Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
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3
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Kaur A, Shuaib S, Goyal D, Goyal B. Interactions of a multifunctional di-triazole derivative with Alzheimer's Aβ42monomer and Aβ42protofibril: a systematic molecular dynamics study. Phys Chem Chem Phys 2020; 22:1543-1556. [DOI: 10.1039/c9cp04775a] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The molecular dynamics simulations results highlighted that the multi-target-directed ligand6nstabilizes the native α-helix conformation of the Aβ42monomer and induces a sizable destabilization in the Aβ42protofibril structure.
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Affiliation(s)
- Anupamjeet Kaur
- Department of Chemistry
- Faculty of Basic and Applied Sciences
- Sri Guru Granth Sahib World University
- Fatehgarh Sahib-140406
- India
| | - Suniba Shuaib
- Department of Chemistry
- Faculty of Basic and Applied Sciences
- Sri Guru Granth Sahib World University
- Fatehgarh Sahib-140406
- India
| | - Deepti Goyal
- Department of Chemistry
- Faculty of Basic and Applied Sciences
- Sri Guru Granth Sahib World University
- Fatehgarh Sahib-140406
- India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry
- Thapar Institute of Engineering & Technology
- Patiala-147004
- India
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4
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Identification of Novel 1,3,5-Triphenylbenzene Derivative Compounds as Inhibitors of Hen Lysozyme Amyloid Fibril Formation. Int J Mol Sci 2019; 20:ijms20225558. [PMID: 31703381 PMCID: PMC6888386 DOI: 10.3390/ijms20225558] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/02/2019] [Indexed: 11/16/2022] Open
Abstract
Deposition of soluble proteins as insoluble amyloid fibrils is associated with a number of pathological states. There is a growing interest in the identification of small molecules that can prevent proteins from undergoing amyloid fibril formation. In the present study, a series of small aromatic compounds with different substitutions of 1,3,5-triphenylbenzene have been synthesized and their possible effects on amyloid fibril formation by hen egg white lysozyme (HEWL), a model protein for amyloid formation, and of their resulting toxicity were examined. The inhibitory effect of the compounds against HEWL amyloid formation was analyzed using thioflavin T and Congo red binding assays, atomic force microscopy, Fourier-transform infrared spectroscopy, and cytotoxicity assays, such as the 3-(4,5-Dimethylthiazol)-2,5-Diphenyltetrazolium Bromide (MTT) reduction assay and caspase-3 activity measurements. We found that all compounds in our screen were efficient inhibitors of HEWL fibril formation and their associated toxicity. We showed that electron-withdrawing substituents such as –F and –NO2 potentiated the inhibitory potential of 1,3,5-triphenylbenzene, whereas electron-donating groups such as –OH, –OCH3, and –CH3 lowered it. These results may ultimately find applications in the development of potential inhibitors against amyloid fibril formation and its biologically adverse effects.
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Sahoo A, Xu H, Matysiak S. Pathways of amyloid-beta absorption and aggregation in a membranous environment. Phys Chem Chem Phys 2019; 21:8559-8568. [PMID: 30964132 DOI: 10.1039/c9cp00040b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aggregation of misfolded oligomeric amyloid-beta (Aβ) peptides on lipid membranes has been identified as a primary event in Alzheimer's pathogenesis. However, the structural and dynamical features of this membrane assisted Aβ aggregation have not been well characterized. The microscopic characterization of dynamic molecular-level interactions in peptide aggregation pathways has been challenging both computationally and experimentally. In this work, we explore differential patterns of membrane-induced Aβ 16-22 (K-L-V-F-F-A-E) aggregation from the microscopic perspective of molecular interactions. Physics-based coarse-grained molecular dynamics (CG-MD) simulations were employed to investigate the effect of lipid headgroup charge - zwitterionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine: POPC) and anionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine: POPS) - on Aβ 16-22 peptide aggregation. Our analyses present an extensive overview of multiple pathways for peptide absorption and biomechanical forces governing peptide folding and aggregation. In agreement with experimental observations, anionic POPS molecules promote extended configurations in Aβ peptides that contribute towards faster emergence of ordered β-sheet-rich peptide assemblies compared to POPC, suggesting faster fibrillation. In addition, lower cumulative rates of peptide aggregation in POPS due to higher peptide-lipid interactions and slower lipid diffusion result in multiple distinct ordered peptide aggregates that can serve as nucleation seeds for subsequent Aβ aggregation. This study provides an in-silico assessment of experimentally observed aggregation patterns, presents new morphological insights and highlights the importance of lipid headgroup chemistry in modulating the peptide absorption and aggregation process.
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Affiliation(s)
- Abhilash Sahoo
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, MD, USA.
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Hilt S, Rojalin T, Viitala T, Koivuniemi A, Bunker A, Hogiu SW, Kálai T, Hideg K, Yliperttula M, Voss JC. Oligomerization Alters Binding Affinity Between Amyloid Beta and a Modulator of Peptide Aggregation. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2017; 121:23974-23987. [PMID: 30214656 PMCID: PMC6130836 DOI: 10.1021/acs.jpcc.7b06164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The soluble oligomeric form of the amyloid beta (Aβ) peptide is the major causative agent in the molecular pathogenesis of Alzheimer's disease (AD). We have previously developed a pyrroline-nitroxyl fluorene compound (SLF) that blocks the toxicity of Aβ. Here we introduce the multi-parametric surface plasmon resonance (MP-SPR) approach to quantify SLF binding and effect on the self-association of the peptide via a label-free, real-time approach. Kinetic analysis of SLF binding to Aβ and measurements of layer thickness alterations inform on the mechanism underlying the ability of SLF to inhibit Aβ toxicity and its progression towards larger oligomeric assemblies. Depending on the oligomeric state of Aβ, distinct binding affinities for SLF are revealed. The Aβ monomer and dimer uniquely possess sub-nanomolar affinity for SLF via a non-specific mode of binding. SLF binding is weaker in oligomeric Aβ, which displays an affinity for SLF on the order of 100 μM. To complement these experiments we carried out molecular docking and molecular dynamics simulations to explore how SLF interacts with the Aβ peptide. The MP-SPR results together with in silico modeling provide affinity data for the SLF-Aβ interaction and allow us to develop a new general method for examining protein aggregation.
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Affiliation(s)
- Silvia Hilt
- Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Tatu Rojalin
- Department of Pathology and Laboratory Medicine, and Center for Biophotonics, University of California Davis, USA
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
| | - Tapani Viitala
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
| | - Artturi Koivuniemi
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
| | - Alex Bunker
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
| | - Sebastian Wachsmann Hogiu
- Department of Pathology and Laboratory Medicine, and Center for Biophotonics, University of California Davis, USA
- Intellectual Ventures/Global Good, Bellevue, WA, USA
| | - Tamás Kálai
- Institute of Organic and Medicinal Chemistry, University of Pécs, H 7624 Pécs, Szigeti st. 12. Pécs, Hungary
| | - Kálmán Hideg
- Institute of Organic and Medicinal Chemistry, University of Pécs, H 7624 Pécs, Szigeti st. 12. Pécs, Hungary
| | - Marjo Yliperttula
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
- Department of Pharmaceutical Sciences, University of Padova, Italy
| | - John C. Voss
- Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA
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7
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Zhang ZX, Hu ZW, Zhao DS, Chen YX, Li YM. Helices with Rational Residues Conduct Different Modulations towards Aβ Aggregation. CHEM LETT 2017. [DOI: 10.1246/cl.170229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Zheng-Xiao Zhang
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Zhi-Wen Hu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - De-Sheng Zhao
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Yong-Xiang Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Yan-Mei Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
- Beijing Institute for Brain Disorders Center of Parkinson’s Disease, P. R. China
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8
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Azam F, Alabdullah NH, Ehmedat HM, Abulifa AR, Taban I, Upadhyayula S. NSAIDs as potential treatment option for preventing amyloid β toxicity in Alzheimer's disease: an investigation by docking, molecular dynamics, and DFT studies. J Biomol Struct Dyn 2017; 36:2099-2117. [PMID: 28571516 DOI: 10.1080/07391102.2017.1338164] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Aggregation of amyloid beta (Aβ) protein considered as one of contributors in development of Alzheimer's disease (AD). Several investigations have identified the importance of non-steroidal anti-inflammatory drugs (NSAIDs) as Aβ aggregation inhibitors. Here, we have examined the binding interactions of 24 NSAIDs belonging to eight different classes, with Aβ fibrils by exploiting docking and molecular dynamics studies. Minimum energy conformation of the docked NSAIDs were further optimized by density functional theory (DFT) employing Becke's three-parameter hybrid model, Lee-Yang-Parr (B3LYP) correlation functional method. DFT-based global reactivity descriptors, such as electron affinity, hardness, softness, chemical potential, electronegativity, and electrophilicity index were calculated to inspect the expediency of these descriptors for understanding the reactive nature and sites of the molecules. Few selected NSAID-Aβ fibrils complexes were subjected to molecular dynamics simulation to illustrate the stability of these complexes and the most prominent interactions during the simulated trajectory. All of the NSAIDs exhibited potential activity against Aβ fibrils in terms of predicted binding affinity. Sulindac was found to be the most active compound underscoring the contribution of indene methylene substitution, whereas acetaminophen was observed as least active NSAID. General structural requirements for interaction of NSAIDs with Aβ fibril include: aryl/heteroaryl aromatic moiety connected through a linker of 1-2 atoms to a distal aromatic group. Considering these structural requirements and electronic features, new potent agents can be designed and developed as potential Aβ fibril inhibitors for the treatment of AD.
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Affiliation(s)
- Faizul Azam
- a Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Misurata University , Misurata , Libya
| | - Nada Hussin Alabdullah
- a Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Misurata University , Misurata , Libya
| | - Hadeel Mohammed Ehmedat
- a Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Misurata University , Misurata , Libya
| | - Abdullah Ramadan Abulifa
- a Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Misurata University , Misurata , Libya
| | - Ismail Taban
- b School of Pharmacy and Pharmaceutical Sciences , Cardiff University , Cardiff , UK
| | - Sreedevi Upadhyayula
- c Department of Chemical Engineering , Indian Institute of Technology , New Delhi , India
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9
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Silva DES, Cali MP, Pazin WM, Carlos-Lima E, Salles Trevisan MT, Venâncio T, Arcisio-Miranda M, Ito AS, Carlos RM. Luminescent Ru(II) Phenanthroline Complexes as a Probe for Real-Time Imaging of Aβ Self-Aggregation and Therapeutic Applications in Alzheimer’s Disease. J Med Chem 2016; 59:9215-9227. [DOI: 10.1021/acs.jmedchem.6b01130] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Debora E. S. Silva
- Departamento
de Química, Universidade Federal de São Carlos, São
Carlos, São Paulo 13565-905, Brazil
| | - Mariana P. Cali
- Departamento
de Química, Universidade Federal de São Carlos, São
Carlos, São Paulo 13565-905, Brazil
| | - Wallance M. Pazin
- Departamento de
Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, USP, Ribeirão Preto, São Paulo 14040-901, Brazil
| | - Estevão Carlos-Lima
- Departamento
de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo 04023-062, Brazil
| | - Maria Teresa Salles Trevisan
- Departamento
de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Ceará Fortaleza, 60451-970, Brazil
| | - Tiago Venâncio
- Departamento
de Química, Universidade Federal de São Carlos, São
Carlos, São Paulo 13565-905, Brazil
| | - Manoel Arcisio-Miranda
- Departamento
de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, São Paulo 04023-062, Brazil
| | - Amando S. Ito
- Departamento de
Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, USP, Ribeirão Preto, São Paulo 14040-901, Brazil
| | - Rose M. Carlos
- Departamento
de Química, Universidade Federal de São Carlos, São
Carlos, São Paulo 13565-905, Brazil
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10
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Mehrazma B, Petoyan A, Opare SK, Rauk A. Interaction of the N-AcAβ(13–23)NH2 segment of the beta amyloid peptide with beta-sheet-blocking peptides: site and edge specificity. CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The region encompassing residues 13–23 of the amyloid beta peptide (Aβ(13–23)) of Alzheimer’s disease is the self-recognition site that initiates toxic oligomerization and fibrillization and also is the site of interaction of Aβ with many other proteins. We describe herein a study by molecular dynamics of the complexes formed by R (= N-AcAβ(13–23)NH2(N-CH3C(O)HHQKLVFFAEDNH2)) with several pseudopeptides designed to form β-sheets with Aβ(1-40,42) and prevent oligomer and fibril formation. Adhesion to both edges of the R β-strand is examined by structure analysis. Umbrella sampling along a dissociation pathway reveals approximate free energies of binding in the submicromolar range. One of the three pseudopeptides binds strongly to one edge of the R β-strand and another to the opposite edge, while the third displays strong binding to both edges. It is desirable to block both edges of the self-recognition site of Aβ to prevent oligomer formation. The study reveals that this may be accomplished by a single pseudopeptide or two in combination. Thus the pseudopeptides, used singly or in pairs, may be competitive inhibitors of Aβ oligomerization at stoichiometric concentrations.
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Affiliation(s)
- Banafsheh Mehrazma
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Anahit Petoyan
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Stanley K.A. Opare
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Arvi Rauk
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
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11
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Hu Z, Wang X, Wang W, Zhang Z, Gao H, Mao Y. Raman spectroscopy for detecting supported planar lipid bilayers composed of ganglioside-GM1/sphingomyelin/cholesterol in the presence of amyloid-β. Phys Chem Chem Phys 2016; 17:22711-20. [PMID: 26256454 DOI: 10.1039/c5cp02366a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The aggregation and fibril formation of amyloid β(Aβ) peptides onto a ganglioside-GM1-containing lipid membrane is a cause of neurodegenerative diseases. The mechanism of the initial binding and the conformational changes of Aβ on the membrane should be clarified. Fluorescence microscopy and Raman spectroscopy have been performed to investigate the supporting planar lipid bilayers (SPBs) composed of ganglioside-GM1, sphingomyelin and cholesterol. It is demonstrated that the SPBs are in a liquid-crystalline state when placed on mica, and increasing the amount of ganglioside-GM1 can decrease the lateral interaction between the acyl chains of the SPBs. It has been found that Aβ(1-40) initially interacts with the galactose ring of the ganglioside-GM1 head group, leading to its binding and gradual aggregation on the membrane surface. The obvious change observed in Raman spectroscopy in the ν(C-H) region confirms that the hydrophobic C-terminal of Aβ(1-40) inserts itself into the hydrophobic part of the SPBs. The Raman data indicate that α-helix and β-sheet structures of Aβ(1-40) increase and coexist over longer time frames. Based on these results, a model was proposed to describe the mechanism of the conformational changes and the aggregation of Aβ(1-40) that are mediated by ganglioside-GM1-containing SPBs.
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Affiliation(s)
- Zhiping Hu
- School of Physics and Electronics, Henan University, Kaifeng 475004, China.
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12
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Investigation of the effect of erythrosine B on amyloid beta peptide using molecular modeling. J Mol Model 2016; 22:92. [DOI: 10.1007/s00894-016-2960-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 03/07/2016] [Indexed: 12/11/2022]
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13
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Khatua P, Jose JC, Sengupta N, Bandyopadhyay S. Conformational features of the Aβ42 peptide monomer and its interaction with the surrounding solvent. Phys Chem Chem Phys 2016; 18:30144-30159. [DOI: 10.1039/c6cp04925g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Heterogeneous conformational flexibility of the Aβ monomers has been found to be correlated with the corresponding non-uniform entropy gains.
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Affiliation(s)
- Prabir Khatua
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
| | - Jaya C. Jose
- Physical Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Neelanjana Sengupta
- Department of Biological Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur-741246
- India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur-721302
- India
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14
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Jose JC, Chatterjee P, Sengupta N. Cross dimerization of amyloid-β and αsynuclein proteins in aqueous environment: a molecular dynamics simulations study. PLoS One 2014; 9:e106883. [PMID: 25210774 PMCID: PMC4161357 DOI: 10.1371/journal.pone.0106883] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/07/2014] [Indexed: 11/18/2022] Open
Abstract
Self-assembly of the intrinsically unstructured proteins, amyloid beta (Aβ) and alpha synclein (αSyn), are associated with Alzheimer's Disease, and Parkinson's and Lewy Body Diseases, respectively. Importantly, pathological overlaps between these neurodegenerative diseases, and the possibilities of interactions between Aβ and αSyn in biological milieu emerge from several recent clinical reports and in vitro studies. Nevertheless, there are very few molecular level studies that have probed the nature of spontaneous interactions between these two sequentially dissimilar proteins and key characteristics of the resulting cross complexes. In this study, we have used atomistic molecular dynamics simulations to probe the possibility of cross dimerization between αSyn1-95 and Aβ1-42, and thereby gain insights into their plausible early assembly pathways in aqueous environment. Our analyses indicate a strong probability of association between the two sequences, with inter-protein attractive electrostatic interactions playing dominant roles. Principal component analysis revealed significant heterogeneity in the strength and nature of the associations in the key interaction modes. In most, the interactions of repeating Lys residues, mainly in the imperfect repeats 'KTKEGV' present in αSyn1-95 were found to be essential for cross interactions and formation of inter-protein salt bridges. Additionally, a hydrophobicity driven interaction mode devoid of salt bridges, where the non-amyloid component (NAC) region of αSyn1-95 came in contact with the hydrophobic core of Aβ1-42 was observed. The existence of such hetero complexes, and therefore hetero assembly pathways may lead to polymorphic aggregates with variations in pathological attributes. Our results provide a perspective on development of therapeutic strategies for preventing pathogenic interactions between these proteins.
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Affiliation(s)
- Jaya C. Jose
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Prathit Chatterjee
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Neelanjana Sengupta
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
- * E-mail:
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15
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Lin D, Luo Y, Wu S, Ma Q, Wei G, Yang X. Investigation of the aggregation process of amyloid-β-(16-22) peptides and the dissolution of intermediate aggregates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:3170-3175. [PMID: 24588450 DOI: 10.1021/la4048165] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The aggregation processes of amyloid-β-(16-22) peptides (Aβ16-22) are investigated by atomic force microscopy (AFM). It is found that Aβ16-22 peptides quickly aggregate from monomers to oligomers and flakelike structures and finally to fibrils. In particular, unusual morphology change is observed in an early stage of aggregation; that is, the originally formed flakelike structures would disappear in the following aggregation processes. To determine the evolution of the flakelike structures, in situ AFM imaging is carried out in liquid to reveal the real-time morphology change of Aβ16-22. The results provide clear evidence that the flakelike structures are in an unstable intermediate state, which would be dissolved into oligomers or short protofibrils for reorganization. Further fluorescence and attenuated total reflectance Fourier transform infrared (ATR-FTIR) experiments on thioflavin T(ThT) suggest that those flakelike structures contain β-sheet components.
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Affiliation(s)
- Dongdong Lin
- State Key Laboratory of Surface Physics, Fudan University , 220 Handan Road, Shanghai 200433, PR China
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16
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Jana AK, Sengupta N. Surface induced collapse of Aβ1-42 with the F19A replacement following adsorption on a single walled carbon nanotube. Biophys Chem 2013; 184:108-15. [DOI: 10.1016/j.bpc.2013.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/25/2013] [Accepted: 09/28/2013] [Indexed: 12/12/2022]
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17
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Ye W, Wang W, Jiang C, Yu Q, Chen H. Molecular dynamics simulations of amyloid fibrils: an in silico approach. Acta Biochim Biophys Sin (Shanghai) 2013; 45:503-8. [PMID: 23532062 DOI: 10.1093/abbs/gmt026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Amyloid fibrils play causal roles in the pathogenesis of amyloid-related degenerative diseases such as Alzheimer's disease, type II diabetes mellitus, and the prion-related transmissible spongiform encephalopathies. The mechanism of fibril formation and protein aggregation is still hotly debated and remains an important open question in order to develop therapeutic method of these diseases. However, traditional molecular biological and crystallographic experiments could hardly observe atomic details and aggregation process. Molecular dynamics (MD) simulations could provide explanations for experimental results and detailed pathway of protein aggregation. In this review, we focus on the applications of MD simulations on several amyloidogenic protein systems. Furthermore, MD simulations could help us to understand the mechanism of amyloid aggregation and how to design the inhibitors.
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Affiliation(s)
- Wei Ye
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China
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18
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Jana AK, Jose JC, Sengupta N. Critical roles of key domains in complete adsorption of Aβ peptide on single-walled carbon nanotubes: insights with point mutations and MD simulations. Phys Chem Chem Phys 2013. [DOI: 10.1039/c2cp42933k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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19
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Juneja A, Ito M, Nilsson L. Implicit Solvent Models and Stabilizing Effects of Mutations and Ligands on the Unfolding of the Amyloid β-Peptide Central Helix. J Chem Theory Comput 2012; 9:834-46. [DOI: 10.1021/ct300941v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alok Juneja
- Department
of Biosciences and Nutrition, Center of
Biosciences, Karolinska Institutet, SE-141 83 Huddinge, Sweden
| | - Mika Ito
- Department
of Biosciences and Nutrition, Center of
Biosciences, Karolinska Institutet, SE-141 83 Huddinge, Sweden
| | - Lennart Nilsson
- Department
of Biosciences and Nutrition, Center of
Biosciences, Karolinska Institutet, SE-141 83 Huddinge, Sweden
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20
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Jana AK, Sengupta N. Adsorption mechanism and collapse propensities of the full-length, monomeric Aβ(1-42) on the surface of a single-walled carbon nanotube: a molecular dynamics simulation study. Biophys J 2012; 102:1889-96. [PMID: 22768945 DOI: 10.1016/j.bpj.2012.03.036] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 03/02/2012] [Accepted: 03/14/2012] [Indexed: 11/25/2022] Open
Abstract
Though nanomaterials such as carbon nanotubes have gained recent attention in biology and medicine, there are few studies at the single-molecule level that explore their interactions with disease-causing proteins. Using atomistic molecular-dynamics simulations, we have investigated the interactions of the monomeric Aβ(1-42) peptide with a single-walled carbon nanotube of small diameter. Starting with peptide-nanotube complexes that delineate the interactions of different segments of the peptide, we find rapid convergence in the peptide's adsorption behavior on the nanotube surface, manifested in its arrested movement, the convergence of peptide-nanotube contact areas and approach distances, and in increased peptide wrapping around the nanotube. In systems where the N-terminal domain is initially distal from nanotube, the adsorption phenomena are initiated by interactions arising from the central hydrophobic core, and precipitated by those arising from the N-terminal residues. Our simulations and free energy calculations together demonstrate that the presence of the nanotube increases the energetic favorability of the open state. We note that the observation of peptide localization could be leveraged for site-specific drug delivery, while the decreased propensity of collapse appears promising for altering kinetics of the peptide's self-assembly.
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Affiliation(s)
- Asis K Jana
- Physical Chemistry Division, National Chemical Laboratory, Pune, India
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21
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Combining conformational sampling and selection to identify the binding mode of zinc-bound amyloid peptides with bifunctional molecules. J Comput Aided Mol Des 2012; 26:963-76. [PMID: 22829296 DOI: 10.1007/s10822-012-9588-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Accepted: 07/05/2012] [Indexed: 01/12/2023]
Abstract
The pathogenesis of Alzheimer's disease (AD) has been suggested to be related with the aggregation of amyloid β (Aβ) peptides. Metal ions (e.g. Cu, Fe, and Zn) are supposed to induce the aggregation of Aβ. Recent development of bifunctional molecules that are capable of interacting with Aβ and chelating biometal ions provides promising therapeutics to AD. However, the molecular mechanism for how Aβ, metal ions, and bifunctional molecules interact with each other is still elusive. In this study, the binding mode of Zn(2+)-bound Aβ with bifunctional molecules was investigated by the combination of conformational sampling of full-length Aβ peptides using replica exchange molecular dynamics simulations (REMD) and conformational selection using molecular docking and classical MD simulations. We demonstrate that Zn(2+)-bound Aβ((1-40)) and Aβ((1-42)) exhibit different conformational ensemble. Both Aβ peptides can adopt various conformations to recognize typical bifunctional molecules with different binding affinities. The bifunctional molecules exhibit their dual functions by first preferentially interfering with hydrophobic residues 17-21 and/or 30-35 of Zn(2+)-bound Aβ. Additional interactions with residues surrounding Zn(2+) could possibly disrupt interactions between Zn(2+) and Aβ, which then facilitate these small molecules to chelate Zn(2+). The binding free energy calculations further demonstrate that the association of Aβ with bifunctional molecules is driven by enthalpy. Our results provide a feasible approach to understand the recognition mechanism of disordered proteins with small molecules, which could be helpful to the design of novel AD drugs.
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22
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Petrlova J, Kálai T, Maezawa I, Altman R, Harishchandra G, Hong HS, Bricarello DA, Parikh AN, Lorigan GA, Jin LW, Hideg K, Voss JC. The influence of spin-labeled fluorene compounds on the assembly and toxicity of the aβ peptide. PLoS One 2012; 7:e35443. [PMID: 22558151 PMCID: PMC3340382 DOI: 10.1371/journal.pone.0035443] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 03/16/2012] [Indexed: 11/18/2022] Open
Abstract
Background The deposition and oligomerization of amyloid β (Aβ) peptide plays a key role in the pathogenesis of Alzheimer's disease (AD). Aβ peptide arises from cleavage of the membrane-associated domain of the amyloid precursor protein (APP) by β and γ secretases. Several lines of evidence point to the soluble Aβ oligomer (AβO) as the primary neurotoxic species in the etiology of AD. Recently, we have demonstrated that a class of fluorene molecules specifically disrupts the AβO species. Methodology/Principal Findings To achieve a better understanding of the mechanism of action of this disruptive ability, we extend the application of electron paramagnetic resonance (EPR) spectroscopy of site-directed spin labels in the Aβ peptide to investigate the binding and influence of fluorene compounds on AβO structure and dynamics. In addition, we have synthesized a spin-labeled fluorene (SLF) containing a pyrroline nitroxide group that provides both increased cell protection against AβO toxicity and a route to directly observe the binding of the fluorene to the AβO assembly. We also evaluate the ability of fluorenes to target multiple pathological processes involved in the neurodegenerative cascade, such as their ability to block AβO toxicity, scavenge free radicals and diminish the formation of intracellular AβO species. Conclusions Fluorene modified with pyrroline nitroxide may be especially useful in counteracting Aβ peptide toxicity, because they posses both antioxidant properties and the ability to disrupt AβO species.
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Affiliation(s)
- Jitka Petrlova
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, United States of America
| | - Tamás Kálai
- Institute of Organic and Medicinal Chemistry, University of Pécs, Pécs, Hungary
| | - Izumi Maezawa
- Laboratory Medicine, Department of Pathology, M.I.N.D. Institute, Miami University, Oxford, Ohio, United States of America
| | - Robin Altman
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, United States of America
| | - Ghimire Harishchandra
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, United States of America
| | - Hyun-Seok Hong
- Laboratory Medicine, Department of Pathology, M.I.N.D. Institute, Miami University, Oxford, Ohio, United States of America
| | - Daniel A. Bricarello
- Department of Applied Science, University of California Davis, Davis, California, United States of America
| | - Atul N. Parikh
- Department of Applied Science, University of California Davis, Davis, California, United States of America
| | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, United States of America
| | - Lee-Way Jin
- Laboratory Medicine, Department of Pathology, M.I.N.D. Institute, Miami University, Oxford, Ohio, United States of America
| | - Kálmán Hideg
- Institute of Organic and Medicinal Chemistry, University of Pécs, Pécs, Hungary
| | - John C. Voss
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, United States of America
- * E-mail:
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23
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Brandenburg E, von Berlepsch H, Gerling UIM, Böttcher C, Koksch B. Inhibition of amyloid aggregation by formation of helical assemblies. Chemistry 2012; 17:10651-61. [PMID: 22003512 DOI: 10.1002/chem.201100670] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The formation of amyloid aggregates is responsible for a wide range of diseases, including Alzheimer's and Parkinson's disease. Although the amyloid-forming proteins have different structures and sequences, all undergo a conformational change to form amyloid aggregates that have a characteristic cross-β-structure. The mechanistic details of this process are poorly understood, but different strategies for the development of inhibitors of amyloid formation have been proposed. In most cases, chemically diverse compounds bind to an elongated form of the protein in a β-strand conformation and thereby exert their therapeutic effect. However, this approach could favor the formation of prefibrillar oligomeric species, which are thought to be toxic. Herein, we report an alternative approach in which a helical coiled-coil-based inhibitor peptide has been designed to engage a coiled-coil-based amyloid-forming model peptide in a stable coiled-coil arrangement, thereby preventing rearrangement into a β-sheet conformation and the subsequent formation of amyloid-like fibrils. Moreover, we show that the helix-forming peptide is able to disassemble mature amyloid-like fibrils.
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24
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Rojas AV, Liwo A, Scheraga HA. A study of the α-helical intermediate preceding the aggregation of the amino-terminal fragment of the β amyloid peptide (Aβ(1-28)). J Phys Chem B 2011; 115:12978-83. [PMID: 21939202 DOI: 10.1021/jp2050993] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The β amyloid (Aβ) peptide aggregates to form β-rich structures that are known to trigger Alzheimer's disease. Experiments suggest that an α-helical intermediate precedes the formation of these aggregates. However, a description at the molecular level of the α-to-β transition has not been obtained. Because it has been proposed that the transition might be initiated in the amino-terminal region of Aβ, we studied the aggregation of the 28-residue amino-terminal fragment of Aβ (Aβ(1-28)) using molecular dynamics and a coarse-grained force field. Simulations starting from extended and helical conformations showed that oligomerization is initiated by the formation of intermolecular β-sheets between the residues in the N-terminal regions. In simulations starting from the α-helical conformation, forcing residues 17-21 to remain in the initial (helical) conformation prevents aggregation but allows for the formation of dimers, indicating that oligomerization, initiated along the nonhelical N-terminal regions, cannot progress without the α-to-β transition propagating along the chains.
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Affiliation(s)
- Ana V Rojas
- Baker Laboratory of Chemistry, Department of Chemistry and Chemical Biology, Cornell Universty, Ithaca, New York 14853-1301, United States
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