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Pseudopeptide Amyloid Aggregation Inhibitors: In Silico, Single Molecule and Cell Viability Studies. Int J Mol Sci 2021; 22:ijms22031051. [PMID: 33494369 PMCID: PMC7865305 DOI: 10.3390/ijms22031051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 11/17/2022] Open
Abstract
Neurodegeneration in Alzheimer's disease (AD) is defined by pathology featuring amyloid-β (Aβ) deposition in the brain. Aβ monomers themselves are generally considered to be nontoxic, but misfold into β-sheets and aggregate to form neurotoxic oligomers. One suggested strategy to treat AD is to prevent the formation of toxic oligomers. The SG inhibitors are a class of pseudopeptides designed and optimized using molecular dynamics (MD) simulations for affinity to Aβ and experimentally validated for their ability to inhibit amyloid-amyloid binding using single molecule force spectroscopy (SMFS). In this work, we provide a review of our previous MD and SMFS studies of these inhibitors and present new cell viability studies that demonstrate their neuroprotective effects against Aβ(1-42) oligomers using mouse hippocampal-derived HT22 cells. Two of the tested SG inhibitors, predicted to bind Aβ in anti-parallel orientation, demonstrated neuroprotection against Aβ(1-42). A third inhibitor, predicted to bind parallel to Aβ, was not neuroprotective. Myristoylation of SG inhibitors, intended to enhance delivery across the blood-brain barrier (BBB), resulted in cytotoxicity. This is the first use of HT22 cells for the study of peptide aggregation inhibitors. Overall, this work will inform the future development of peptide aggregation inhibitors against Aβ toxicity.
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Liu H, Sun Y, Li Z, Yang R, Yang J, Aryee AA, Zhang X, Ge J, Qu L, Lin Y. SciFinder-guided rational design of fluorescent carbon dots for ratiometric monitoring intracellular pH fluctuations under heat shock. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.06.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Opare SKA, Rauk A. Pseudopeptide Designed to Inhibit Oligomerization and Redox Chemistry in Alzheimer’s Disease. J Phys Chem B 2019; 123:5206-5215. [DOI: 10.1021/acs.jpcb.9b01665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stanley K. A. Opare
- Department of Chemistry, The University of Calgary, Calgary, Alberta Canada, T2N 1N4
| | - Arvi Rauk
- Department of Chemistry, The University of Calgary, Calgary, Alberta Canada, T2N 1N4
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Mehrazma B, Opare S, Petoyan A, Rauk A. d-Amino Acid Pseudopeptides as Potential Amyloid-Beta Aggregation Inhibitors. Molecules 2018; 23:E2387. [PMID: 30231520 PMCID: PMC6225248 DOI: 10.3390/molecules23092387] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/06/2018] [Accepted: 09/14/2018] [Indexed: 12/18/2022] Open
Abstract
A causative factor for neurotoxicity associated with Alzheimer's disease is the aggregation of the amyloid-β (Aβ) peptide into soluble oligomers. Two all d-amino acid pseudo-peptides, SGB1 and SGD1, were designed to stop the aggregation. Molecular dynamics (MD) simulations have been carried out to study the interaction of the pseudo-peptides with both Aβ13⁻23 (the core recognition site of Aβ) and full-length Aβ1⁻42. Umbrella sampling MD calculations have been used to estimate the free energy of binding, ∆G, of these peptides to Aβ13⁻23. The highest ∆Gbinding is found for SGB1. Each of the pseudo-peptides was also docked to Aβ1⁻42 and subjected up to seven microseconds of all atom molecular dynamics simulations. The resulting structures lend insight into how the dynamics of Aβ1⁻42 are altered by complexation with the pseudo-peptides and confirmed that SGB1 may be a better candidate for developing into a drug to prevent Alzheimer's disease.
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Affiliation(s)
- Banafsheh Mehrazma
- Department of Chemistry, University of Calgary; Calgary, AB T2N 1N4, Canada.
| | - Stanley Opare
- Department of Chemistry, University of Calgary; Calgary, AB T2N 1N4, Canada.
| | - Anahit Petoyan
- Department of Chemistry, University of Calgary; Calgary, AB T2N 1N4, Canada.
| | - Arvi Rauk
- Department of Chemistry, University of Calgary; Calgary, AB T2N 1N4, Canada.
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Pseudo-peptide amyloid-β blocking inhibitors: molecular dynamics and single molecule force spectroscopy study. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1707-1718. [PMID: 28844735 DOI: 10.1016/j.bbapap.2017.07.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/07/2017] [Accepted: 07/25/2017] [Indexed: 12/14/2022]
Abstract
By combining MD simulations and AFS experimental technique, we demonstrated a powerful approach for rational design and single molecule testing of novel inhibitor molecules which can block amyloid-amyloid binding - the first step of toxic amyloid oligomer formation. We designed and tested novel pseudo-peptide amyloid-β (Aβ) inhibitors that bind to the Aβ peptide and effectively prevent amyloid-amyloid binding. First, molecular dynamics (MD) simulations have provided information on the structures and binding characteristics of the designed pseudo-peptides targeting amyloid fragment Aβ (13-23). The binding affinities between the inhibitor and Aβ as well as the inhibitor to itself have been estimated using Umbrella Sampling calculations. Atomic Force Spectroscopy (AFS) was used to experimentally test several proposed inhibitors in their ability to block amyloid-amyloid binding - the first step of toxic amyloid oligomer formation. The experimental AFS data are in a good agreement with theoretical MD calculations and demonstrate that three proposed pseudo-peptides bind to amyloid fragment with different affinities and all effectively prevent Aβ-Aβ binding in similar way. We propose that the designed pseudo-peptides can be used as potential drug candidates to prevent Aβ toxicity in Alzheimer's disease.
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Shi H, Lee JY. Tautomeric Effect of Histidine on the Monomeric Structure of Amyloid β-Peptide(1-42). ACS Chem Neurosci 2017; 8:669-675. [PMID: 28292182 DOI: 10.1021/acschemneuro.6b00375] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Tautomeric state of histidine is one of the factors that influence the structural and aggregation properties of amyloid β (Aβ)-peptide in neutral state. It is worth it to uncover the monomeric properties of Aβ(1-42) peptide in comparison with Aβ(1-40) peptide. Our replica-exchange molecular dynamics simulations results show that the sheet content of each tautomeric isomer in Aβ(1-42) monomer is slightly higher than that in Aβ(1-40) monomer except His6(δ)-His13(δ)-His14(δ) (δδδ) isomer, implying higher aggregation tendency in Aβ(1-42), which is in agreement with previous experimental and theoretical studies. Further analysis indicates that (εεε), (εδε), (εδδ), and (δδε) isomers prefer sheet conformation although they are in nondominating states. Particularly, it is confirmed that antiparallel β-sheets of (εδδ) were formed at K16-E22 (22.0-43.9%), N27-A30 except G29 (21.9-40.2%), and M35-I41 except G37 (24.1-43.4%). Furthermore, (εδδ) may be the easiest one to overcome structural transformation due to nonobstructing interactions between K16 and/or L17 and histidine residues. The current study will help to understand the tautomeric effect of Aβ(1-42) peptide to overcome Alzheimer's disease.
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Affiliation(s)
- Hu Shi
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
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Shi H, Kang B, Lee JY. Tautomeric Effect of Histidine on the Monomeric Structure of Amyloid β-Peptide(1–40). J Phys Chem B 2016; 120:11405-11411. [DOI: 10.1021/acs.jpcb.6b08685] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Hu Shi
- Department
of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Baotao Kang
- Department
of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Jin Yong Lee
- Department
of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
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Amini Z, Fatemi MH, Rauk A. Molecular dynamics studies of a β-sheet blocking peptide with the full-length amyloid beta peptide of Alzheimer’s disease. CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0267] [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. A number of pseudopeptides have been designed to bind to Aβ(13–23) and been computationally shown to do so with high affinity. More interactions are available in full-length Aβ than are available in the shorter peptide. We describe herein a study by molecular dynamics (MD) of nine distinct complexes formed by one such pseudopeptide, SGA1, with full-length beta amyloid, Aβ(1–42). The relative stabilities of the Aβ–SGA1 complexes were estimated by a combination of MD and ab initio methods. The most stable complex, designated AB1, was found to be one in which SGA1 is bound to the self-recognition site of Aβ(1–42) in an antiparallel β-sheet fashion. Another complex, designated AB3, also involved SGA1 binding to the self-recognition region of Aβ(1–42), albeit with lower affinity. In both AB1 and AB3, SGA1 formed antiparallel β-sheets but to opposite edges of Aβ. A complex, AB4, with similar stability to AB3, was found with a parallel β-sheet in the self-recognition site. A fourth complex, AB7, also with similar stability, formed a parallel β-sheet in the hydrophobic central region of Aβ. In all cases, complexation of SGA1 induced extensive β-sheet structure in Aβ(1–42).
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Affiliation(s)
- Zohreh Amini
- Chemometrics Laboratory, Faculty of Chemistry, University of Mazandaran, Babolsar, Mazandaran 47416-95447, Iran
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Mohammad Hossein Fatemi
- Chemometrics Laboratory, Faculty of Chemistry, University of Mazandaran, Babolsar, Mazandaran 47416-95447, Iran
| | - Arvi Rauk
- Department of Chemistry, University of Calgary, Calgary, AB T2N 1N4, Canada
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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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