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Park C, Kim K, Kim Y, Zhu R, Hain L, Seferovic H, Kim MH, Woo HJ, Hwang H, Lee SH, Kim S, Lee JE, Hinterdorfer P, Ko K, Park S, Oh YJ. Plant-Derived Anti-Human Epidermal Growth Factor Receptor 2 Antibody Suppresses Trastuzumab-Resistant Breast Cancer with Enhanced Nanoscale Binding. ACS NANO 2024. [PMID: 38764224 DOI: 10.1021/acsnano.4c00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Traditional monoclonal antibodies such as Trastuzumab encounter limitations when treating Human Epidermal Growth Factor Receptor 2 (HER2)-positive breast cancer, particularly in cases that develop resistance. This study introduces plant-derived anti-HER2 variable fragments of camelid heavy chain domain (VHH) fragment crystallizable region (Fc) KEDL(K) antibody as a potent alternative for overcoming these limitations. A variety of biophysical techniques, in vitro assays, and in vivo experiments uncover the antibody's nanoscale binding dynamics with transmembrane HER2 on living cells. Single-molecule force spectroscopy reveals the rapid formation of two robust bonds, exhibiting approximately 50 pN force resistance and bond lifetimes in the second range. The antibody demonstrates a specific affinity for HER2-positive breast cancer cells, including those that are Trastuzumab-resistant. Moreover, in immune-deficient mice, the plant-derived anti-HER2 VHH-FcK antibody exhibits superior antitumor activity, especially against tumors that are resistant to Trastuzumab. These findings underscore the plant-derived antibody's potential as an impactful immunotherapeutic strategy for treating Trastuzumab-resistant HER2-positive breast cancer.
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Affiliation(s)
- Chanyong Park
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea
| | - Kibum Kim
- Department of Medicine, Medical Research Institute, College of Medicine, Chung-Ang University, Seoul 06974, Korea
| | - Yerin Kim
- Department of Medicine, Medical Research Institute, College of Medicine, Chung-Ang University, Seoul 06974, Korea
| | - Rong Zhu
- Department of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, 4040 Linz, Austria
| | - Lisa Hain
- Department of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, 4040 Linz, Austria
| | - Hannah Seferovic
- Department of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, 4040 Linz, Austria
| | - Min-Hyeok Kim
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea
| | - Hyun Joo Woo
- Major of Nano-Bioengineering, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea
| | - Hyunju Hwang
- Department of Medicine, Medical Research Institute, College of Medicine, Chung-Ang University, Seoul 06974, Korea
| | - Seung Ho Lee
- Major of Nano-Bioengineering, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea
| | - Sangmin Kim
- Department of Breast Cancer Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Jeong Eon Lee
- Division of Breast Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Peter Hinterdorfer
- Department of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, 4040 Linz, Austria
| | - Kisung Ko
- Department of Medicine, Medical Research Institute, College of Medicine, Chung-Ang University, Seoul 06974, Korea
| | - Sungsu Park
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea
| | - Yoo Jin Oh
- Department of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, 4040 Linz, Austria
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2
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Okumura H. Perspective for Molecular Dynamics Simulation Studies of Amyloid-β Aggregates. J Phys Chem B 2023; 127:10931-10940. [PMID: 38109338 DOI: 10.1021/acs.jpcb.3c06051] [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: 12/20/2023]
Abstract
The cause of Alzheimer's disease is related to aggregates such as oligomers and amyloid fibrils consisting of amyloid-β (Aβ) peptides. Molecular dynamics (MD) simulation studies have been conducted to understand the molecular mechanism of the formation and disruption of Aβ aggregates. In this Perspective, the MD simulation studies are classified into four categories, focusing on the target systems: aggregation of Aβ peptides in bulk solution, Aβ aggregation at the interface, aggregation inhibitor against Aβ peptides, and nonequilibrium MD simulation of Aβ aggregates. MD simulation studies in these categories are first reviewed. Future perspectives in each category are then presented. Finally, the overall perspective is presented on how MD simulations of Aβ aggregates can be utilized for developing Alzheimer's disease treatment.
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Affiliation(s)
- Hisashi Okumura
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Okazaki, Aichi 444-8787, Japan
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3
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Lazarev VF, Dutysheva EA, Kanunikov IE, Guzhova IV, Margulis BA. Protein Interactome of Amyloid-β as a Therapeutic Target. Pharmaceuticals (Basel) 2023; 16:312. [PMID: 37259455 PMCID: PMC9965366 DOI: 10.3390/ph16020312] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/27/2023] [Accepted: 02/08/2023] [Indexed: 04/12/2024] Open
Abstract
The amyloid concept of Alzheimer's disease (AD) assumes the β-amyloid peptide (Aβ) as the main pathogenic factor, which injures neural and other brain cells, causing their malfunction and death. Although Aβ has been documented to exert its cytotoxic effect in a solitary manner, there is much evidence to claim that its toxicity can be modulated by other proteins. The list of such Aβ co-factors or interactors includes tau, APOE, transthyretin, and others. These molecules interact with the peptide and affect the ability of Aβ to form oligomers or aggregates, modulating its toxicity. Thus, the list of potential substances able to reduce the harmful effects of the peptide should include ones that can prevent the pathogenic interactions by specifically binding Aβ and/or its partners. In the present review, we discuss the data on Aβ-based complexes in AD pathogenesis and on the compounds directly targeting Aβ or the destructors of its complexes with other polypeptides.
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Affiliation(s)
- Vladimir F. Lazarev
- Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia
| | - Elizaveta A. Dutysheva
- Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia
| | - Igor E. Kanunikov
- Biological Faculty, St. Petersburg State University, 199034 Saint Petersburg, Russia
| | - Irina V. Guzhova
- Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia
| | - Boris A. Margulis
- Institute of Cytology of the Russian Academy of Sciences, 194064 Saint Petersburg, Russia
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4
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Sun H, Wang J. Novel perspective for protein-drug interaction analysis: atomic force microscope. Analyst 2023; 148:454-474. [PMID: 36398684 DOI: 10.1039/d2an01591a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Proteins are major drug targets, and drug-target interaction identification and analysis are important factors for drug discovery. Atomic force microscopy (AFM) is a powerful tool making it possible to image proteins with nanometric resolution and probe intermolecular forces under physiological conditions. We review recent studies conducted in the field of target protein drug discovery using AFM-based analysis technology, including drug-driven changes in nanomechanical properties of protein morphology and interactions. Underlying mechanisms (including thermodynamic and kinetic parameters) of the drug-target interaction and drug-modulating protein-protein interaction (PPI) on the surfaces of models or living cells are discussed. Furthermore, challenges and the outlook for the field are likewise discussed. Overall, this insight into the mechanical properties of protein-drug interactions provides an unprecedented information framework for rational drug discovery in the pharmaceutical field.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
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Robinson MJ, Newbury S, Singh K, Leonenko Z, Beazely MA. The Interplay Between Cholesterol and Amyloid-β on HT22 Cell Viability, Morphology, and Receptor Tyrosine Kinase Signaling. J Alzheimers Dis 2023; 96:1663-1683. [PMID: 38073391 DOI: 10.3233/jad-230753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
BACKGROUND There is a lack of understanding in the molecular and cellular mechanisms of Alzheimer's disease that has hindered progress on therapeutic development. The focus has been on targeting toxic amyloid-β (Aβ) pathology, but these therapeutics have generally failed in clinical trials. Aβ is an aggregation-prone protein that has been shown to disrupt cell membrane structure in molecular biophysics studies and interfere with membrane receptor signaling in cell and animal studies. Whether the lipid membrane or specific receptors are the primary target of attack has not been determined. OBJECTIVE This work elucidates some of the interplay between membrane cholesterol and Aβ42 on HT22 neuronal cell viability, morphology, and platelet-derived growth factor (PDGF) signaling pathways. METHODS The effects of cholesterol depletion by methyl-β-cyclodextrin followed by treatment with Aβ and/or PDGF-AA were assessed by MTT cell viability assays, western blot, optical and AFM microscopy. RESULTS Cell viability studies show that cholesterol depletion was mildly protective against Aβ toxicity. Together cholesterol reduction and Aβ42 treatment compounded the disruption of the PDGFα receptor activation. Phase contrast optical microscopy and live cell atomic force microscopy imaging revealed that cytotoxic levels of Aβ42 caused morphological changes including cell membrane damage, cytoskeletal disruption, and impaired cell adhesion; cell damage was ameliorated by cellular cholesterol depletion. CONCLUSIONS Cholesterol depletion impacted the effects of Aβ42 on HT22 cell viability, morphology, and receptor tyrosine kinase signaling.
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Affiliation(s)
- Morgan J Robinson
- School of Pharmacy, University of Waterloo, Waterloo, ON, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Sean Newbury
- School of Pharmacy, University of Waterloo, Waterloo, ON, Canada
| | - Kartar Singh
- School of Pharmacy, University of Waterloo, Waterloo, ON, Canada
| | - Zoya Leonenko
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- Department of Physics and Astronomy, University of Waterloo, Waterloo, ON, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Michael A Beazely
- School of Pharmacy, University of Waterloo, Waterloo, ON, Canada
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
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Linking Cerebrovascular Dysfunction to Age-Related Hearing Loss and Alzheimer’s Disease—Are Systemic Approaches for Diagnosis and Therapy Required? Biomolecules 2022; 12:biom12111717. [DOI: 10.3390/biom12111717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/09/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Alzheimer’s disease (AD), the most common cause of dementia in the elderly, is a neurodegenerative disorder associated with neurovascular dysfunction, cognitive decline, and the accumulation of amyloid β peptide (Aβ) in the brain and tau-related lesions in neurons termed neurofibrillary tangles (NFTs). Aβ deposits and NFT formation are the central pathological hallmarks in AD brains, and the majority of AD cases have been shown to exhibit a complex combination of systemic comorbidities. While AD is the foremost common cause of dementia in the elderly, age-related hearing loss (ARHL) is the most predominant sensory deficit in the elderly. During aging, chronic inflammation and resulting endothelial dysfunction have been described and might be key contributors to AD; we discuss an intriguing possible link between inner ear strial microvascular pathology and blood–brain barrier pathology and present ARHL as a potentially modifiable and treatable risk factor for AD development. We present compelling evidence that ARHL might well be seen as an important risk factor in AD development: progressive hearing impairment, leading to social isolation, and its comorbidities, such as frailty, falls, and late-onset depression, link ARHL with cognitive decline and increased risk of dementia, rendering it tempting to speculate that ARHL might be a potential common molecular and pathological trigger for AD. Additionally, one could speculate that amyloid-beta might damage the blood–labyrinth barrier as it does to the blood–brain barrier, leading to ARHL pathology. Finally, there are options for the treatment of ARHL by targeted neurotrophic factor supplementation to the cochlea to improve cognitive outcomes; they can also prevent AD development and AD-related comorbidity in the future.
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Shityakov S, Hayashi K, Störk S, Scheper V, Lenarz T, Förster CY. The Conspicuous Link between Ear, Brain and Heart-Could Neurotrophin-Treatment of Age-Related Hearing Loss Help Prevent Alzheimer's Disease and Associated Amyloid Cardiomyopathy? Biomolecules 2021; 11:biom11060900. [PMID: 34204299 PMCID: PMC8235707 DOI: 10.3390/biom11060900] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/05/2021] [Accepted: 06/14/2021] [Indexed: 12/23/2022] Open
Abstract
Alzheimer's disease (AD), the most common cause of dementia in the elderly, is a neurodegenerative disorder associated with neurovascular dysfunction and cognitive decline. While the deposition of amyloid β peptide (Aβ) and the formation of neurofibrillary tangles (NFTs) are the pathological hallmarks of AD-affected brains, the majority of cases exhibits a combination of comorbidities that ultimately lead to multi-organ failure. Of particular interest, it can be demonstrated that Aβ pathology is present in the hearts of patients with AD, while the formation of NFT in the auditory system can be detected much earlier than the onset of symptoms. Progressive hearing impairment may beget social isolation and accelerate cognitive decline and increase the risk of developing dementia. The current review discusses the concept of a brain-ear-heart axis by which Aβ and NFT inhibition could be achieved through targeted supplementation of neurotrophic factors to the cochlea and the brain. Such amyloid inhibition might also indirectly affect amyloid accumulation in the heart, thus reducing the risk of developing AD-associated amyloid cardiomyopathy and cardiovascular disease.
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Affiliation(s)
- Sergey Shityakov
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine, University Hospital Würzburg, D-97080 Würzburg, Germany;
- Infochemistry Scientific Center, Laboratory of Chemoinformatics, ITMO University, 191002 Saint-Petersburg, Russia
| | - Kentaro Hayashi
- Advanced Stroke Center, Shimane University Hospital, 89-1 Enya, Shimane, Izumo 693-8501, Japan;
| | - Stefan Störk
- Comprehensive Heart Failure Q9 Center, University of Würzburg, D-97080 Würzburg, Germany;
| | - Verena Scheper
- Department of Otolaryngology, Hannover Medical School and Cluster of Excellence “Hearing4All”, 30625 Hannover, Germany;
| | - Thomas Lenarz
- Department of Otolaryngology, Hannover Medical School and Cluster of Excellence “Hearing4All”, 30625 Hannover, Germany;
- Correspondence: (T.L.); (C.Y.F.)
| | - Carola Y. Förster
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine, University Hospital Würzburg, D-97080 Würzburg, Germany;
- Correspondence: (T.L.); (C.Y.F.)
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8
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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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Yoon J, Kim Y, Park JW. Binary Structure of Amyloid Beta Oligomers Revealed by Dual Recognition Mapping. Anal Chem 2019; 91:8422-8428. [PMID: 31140786 DOI: 10.1021/acs.analchem.9b01316] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Amyloid beta (Aβ) oligomers are widely considered to be the causative agent of Alzheimer's disease (AD), a progressive neurodegenerative disorder. Determining the structure of oligomers is, therefore, important for understanding the disease and developing therapeutic agents; however, elucidating the structure has been proven difficult due to heterogeneity, noncrystallinity, and variability. Herein, we investigated homo- and hetero-oligomers of Aβ40 and Aβ42 using atomic force microscopy (AFM) and revealed characteristics of the molecular structure. By examining the surface of individual oligomers with sequential N- and C-terminus specific antibody-tethered tips, we simultaneously mapped the N- and C-terminus distributions and the elastic modulus. Interestingly, both the N- and C-termini of Aβ peptides were recognized on the oligomer surface, and the termini detected pixel regions exhibited a lower elastic modulus than silent pixel regions. These two types of regions were randomly distributed on the oligomer surface.
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Affiliation(s)
- Jihyun Yoon
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Youngkyu Kim
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Joon Won Park
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
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Karimi H, Heydari Dokoohaki M, Zolghadr AR, Ghatee MH. The interactions of an Aβ protofibril with a cholesterol-enriched membrane and involvement of neuroprotective carbazolium-based substances. Phys Chem Chem Phys 2019; 21:11066-11078. [PMID: 31090756 DOI: 10.1039/c9cp00859d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Recent studies have shown that the aggregation of the amyloid-beta peptide (Aβ) in the brain cell membrane is responsible for the emergence of Alzheimer's disease (AD); the exploration of effective factors involved in the extension of the aggregation process and alternatively the examination of an effective inhibitor via theoretical and experimental tools are among the main research topics in the field of AD treatment. Therefore, in this study, we used all-atom molecular dynamics (MD) simulations to clarify the impact of cell membrane cholesterol on the interaction of Aβ with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) as a membrane model. Moreover, the effect of the P7C3-S243 molecule on the abovementioned process was investigated. The simulation results disclosed the neuroprotective property of the P7C3-S243 molecule. The MD simulation results indicate that the interaction of cholesterol molecules with the Aβ oligomer is negligible and cannot enhance membrane rupture. However, strong hydrogen bonding between the POPC molecules and the oligomers led to membrane perturbation. According to our modellings, the P7C3-S243 molecular layer can protect the cell membrane by inhibiting the direct interaction between the bilayer and Aβ. In addition, free-energy calculations were conducted to determine the possible penetration of Aβ fibrils into the cholesterol-enriched membrane.
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Affiliation(s)
- Hedayat Karimi
- Department of Chemistry, Shiraz University, Shiraz, 71946-84795, Iran.
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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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Affiliation(s)
- Stanley K. A. Opare
- Department of Chemistry, University of Calgary, 2500 University Drive Northwest, Calgary, Alberta, Canada T2N 1N4
| | - Arvi Rauk
- Department of Chemistry, University of Calgary, 2500 University Drive Northwest, Calgary, Alberta, Canada T2N 1N4
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