1
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Shen H, Liu K, Kong F, Ren M, Wang X, Wang S. Strategies for measuring concentrations and forms of amyloid-β peptides. Biosens Bioelectron 2024; 259:116405. [PMID: 38776801 DOI: 10.1016/j.bios.2024.116405] [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] [Received: 01/31/2024] [Revised: 05/01/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Alzheimer's disease (AD) is affecting more and more people worldwide without the effective treatment, while the existed pathological mechanism has been confirmed barely useful in the treatment. Amyloid-β peptide (Aβ), a main component of senile plaque, is regarded as the most promising target in AD treatment. Aβ clearance from AD brain seems to be a reliably therapeutic strategy, as the two exited drugs, GV-971 and aducanumab, are both developed based on it. However, doubt still exists. To exhaustive expound on the pathological mechanism of Aβ, rigorous analyses on the concentrations and aggregation forms are essential. Thus, it is attracting broad attention these years. However, most of the sensors have not been used in pathological studies, as the lack of the bridge between analytical chemist and pathologists. In this review, we made a brief introduce on Aβ-related pathological mechanism included in β-amyloid hypothesis to elucidate the detection conditions of sensor methods. Furthermore, a summary of the sensor methods was made, which were based on Aβ concentrations and form detections that have been developed in the past 10 years. As the greatest number of the sensors were built on fluorescent spectroscopy, electrochemistry, and Roman spectroscopy, detailed elucidation on them was made. Notably, the aggregation process is another important factor in revealing the progress of AD and developing the treatment methods, so the sensors on monitoring Aβ aggregation processes were also summarized.
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Affiliation(s)
- Hangyu Shen
- State Key Laboratory of Biobased Materials and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250353, PR China
| | - Keyin Liu
- State Key Laboratory of Biobased Materials and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250353, PR China
| | - Fangong Kong
- State Key Laboratory of Biobased Materials and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250353, PR China
| | - Mingguang Ren
- State Key Laboratory of Biobased Materials and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250353, PR China
| | - Xiaoying Wang
- State Key Laboratory of Biobased Materials and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250353, PR China; Shandong Haizhibao Ocean Technology Co., Ltd, Weihai, Shandong, 264333, PR China.
| | - Shoujuan Wang
- State Key Laboratory of Biobased Materials and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250353, PR China.
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2
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Hickey JP, Collins AE, Nelson ML, Chen H, Kalisch BE. Modulation of Oxidative Stress and Neuroinflammation by Cannabidiol (CBD): Promising Targets for the Treatment of Alzheimer's Disease. Curr Issues Mol Biol 2024; 46:4379-4402. [PMID: 38785534 PMCID: PMC11120237 DOI: 10.3390/cimb46050266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease and the most common form of dementia globally. Although the direct cause of AD remains under debate, neuroinflammation and oxidative stress are critical components in its pathogenesis and progression. As a result, compounds like cannabidiol (CBD) are being increasingly investigated for their ability to provide antioxidant and anti-inflammatory neuroprotection. CBD is the primary non-psychotropic phytocannabinoid derived from Cannabis sativa. It has been found to provide beneficial outcomes in a variety of medical conditions and is gaining increasing attention for its potential therapeutic application in AD. CBD is not psychoactive and its lipophilic nature allows its rapid distribution throughout the body, including across the blood-brain barrier (BBB). CBD also possesses anti-inflammatory, antioxidant, and neuroprotective properties, making it a viable candidate for AD treatment. This review outlines CBD's mechanism of action, the role of oxidative stress and neuroinflammation in AD, and the effectiveness and limitations of CBD in preclinical models of AD.
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Affiliation(s)
| | | | | | | | - Bettina E. Kalisch
- Department of Biomedical Sciences and Collaborative Specialization in Neuroscience Program, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.P.H.); (A.E.C.); (M.L.N.); (H.C.)
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3
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Pehlivan Ö, Wojtkowiak K, Jezierska A, Waliczek M, Stefanowicz P. Photochemical Transformations of Peptides Containing the N-(2-Selenoethyl)glycine Moiety. ACS OMEGA 2024; 9:16775-16791. [PMID: 38617632 PMCID: PMC11007844 DOI: 10.1021/acsomega.4c01015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/16/2024]
Abstract
The diselenide bond has attracted considerable attention due to its ability to undergo the metathesis reaction in response to visible light. In our previous study, we demonstrated visible-light-induced diselenide metathesis of selenocysteine-containing linear peptides, allowing for the convenient generation of peptide libraries. Here, we investigated the transformation of linear and cyclic peptides containing the N-(2-selenoethyl)glycine moiety. The linear peptides were highly susceptible to the metathesis reaction, whereas the cyclic systems gave only limited conversion yields of the metathesis product. In both cases, side reactions leading to the formation of mono-, di-, and polyselenides were observed upon prolonged irradiation. To confirm the radical mechanism of the reaction, the radical initiator 2,2'-azobis[2-(2-imidazolin-2-yl)propane] dihydrochloride (VA-044) was tested, and it was found to induce diselenide metathesis without photochemical activation. The data were interpreted in the light of quantum-chemical simulations based on density functional theory (DFT). The simulations were performed at the B3LYP-D3BJ/def2-TZVP level of theory using a continuum solvation model (IEF-PCM) and methanol as a solvent.
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Affiliation(s)
- Özge Pehlivan
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie str. 14, 50-383 Wrocław, Poland
| | - Kamil Wojtkowiak
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie str. 14, 50-383 Wrocław, Poland
| | - Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie str. 14, 50-383 Wrocław, Poland
| | - Mateusz Waliczek
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie str. 14, 50-383 Wrocław, Poland
| | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie str. 14, 50-383 Wrocław, Poland
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4
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De Santis E, Alleva S, Minicozzi V, Morante S, Stellato F. Probing the Dynamic Landscape: From Static to Time-Resolved X-Ray Absorption Spectroscopy to Investigate Copper Redox Chemistry in Neurodegenerative Disorders. Chempluschem 2024:e202300712. [PMID: 38526934 DOI: 10.1002/cplu.202300712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
Copper (Cu), with its ability to exist in various oxidation states, notably Cu(I) and Cu(II), plays a crucial role in diverse biological redox reactions. This includes its involvement in pathways associated with oxidative stress in neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and Transmissible Spongiform Encephalopathies. This paper offers an overview of X-ray Absorption Spectroscopy (XAS) studies designed to elucidate the interactions between Cu ions and proteins or peptides associated with these neurodegenerative diseases. The emphasis lies on XAS specificity, revealing the local coordination environment, and on its sensitivity to Cu oxidation states. Furthermore, the paper focuses on XAS applications targeting the characterization of intermediate reaction states and explores the opportunities arising from recent advancements in time-resolved XAS at ultrabright synchrotron and Free Electron Laser radiation sources.
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Affiliation(s)
- Emiliano De Santis
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Stefania Alleva
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
| | - Velia Minicozzi
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
| | - Silvia Morante
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
| | - Francesco Stellato
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
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5
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Lou H, Zhang Y, Kuczera K, Hageman MJ, Schöneich C. Molecular Dynamics Simulation of an Iron(III) Binding Site on the Fc Domain of IgG1 Relevant for Visible Light-Induced Protein Fragmentation. Mol Pharm 2024; 21:501-512. [PMID: 38128475 DOI: 10.1021/acs.molpharmaceut.3c00612] [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: 12/23/2023]
Abstract
Molecular dynamics simulations were employed to investigate the interaction between Fe(III) and an iron-binding site composed of THR259, ASP252, and GLU261 on the Fc domain of an IgG1. The goal was to provide microscopic mechanistic information for the photochemical, iron-dependent site-specific oxidative fragmentation of IgG1 at THR259 reported in our previous paper. The distance between Fe(III) and residues of interest as well as the binding pocket size was examined for both protonated and deprotonated THR259. The Fe(III) binding free energy (ΔG) was estimated by using an umbrella sampling approach. The pKa shift of the THR259 hydroxyl group caused by the presence of nearby Fe(III) was estimated based on a thermodynamic cycle. The simulation results show that Fe(III) resides inside the proposed binding pocket and profoundly changes the pocket configuration. The ΔG values indicate that the pocket possesses a strong binding affinity for Fe(III). Furthermore, Fe(III) profoundly lowers the pKa value of the THR259 hydroxyl group by 5.4 pKa units.
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Affiliation(s)
- Hao Lou
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
- Biopharmaceutical Innovation and Optimization Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - Yilue Zhang
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Krzysztof Kuczera
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Michael J Hageman
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
- Biopharmaceutical Innovation and Optimization Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - Christian Schöneich
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
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6
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Sunda AP, Sharma AK. Molecular Insights into Cu/Zn Metal Response to the Amyloid β-Peptide (1-42). ACS PHYSICAL CHEMISTRY AU 2024; 4:57-66. [PMID: 38283784 PMCID: PMC10811771 DOI: 10.1021/acsphyschemau.3c00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 01/30/2024]
Abstract
Aβ1-40 peptide and Aβ1-42 peptide are the building units of beta-amyloid plaques present in Alzheimer's disease (AD)-affected brain. The binding affinity of various divalent metal ions such as Cu and Zn present in AD-affected brain with different amino acids available in Aβ-peptide became the focus to explore their role in soluble neurotoxic oligomer formation. Cu2+ metal ions are known to enhance the neurotoxicity of the Aβ1-42 peptide by catalyzing the formation of soluble neurotoxic oligomers. The competitive preference of both Cu2+ and Zn2+ simultaneously to interact with the Aβ-peptide is unknown. The divalent Cu and Zn ions were inserted in explicit aqueous Aβ1-42 peptide configurations to get insights into the binding competence of these metal ions with peptides using classical molecular dynamics (MD) simulations. The metal-ion interactions reveal that competitive binding preferences of various peptide sites become metal-ion-specific and differ significantly. For Cu2+, interactions are found to be more significant with respect to those of Asp-7, His-6, Glu-11, and His-14. Asp-1, Glu-3, Asp-7, His-6, Glu-11, and His-13 amino acid residues show higher affinity toward Zn2+ ions. MD simulations show notable variation in the solvent-accessible surface area in the hydrophobic region of the peptide. Infinitesimal mobility was obtained for Zn2+ compared to Cu2+ in an aqueous solution and Cu2+ diffusivity deviated significantly at different time scales, proving its labile features in aqueous Aβ1-42 peptides.
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Affiliation(s)
- Anurag Prakash Sunda
- Department
of Chemistry, J. C. Bose University of Science
and Technology, YMCA, Faridabad 121006, India
| | - Anuj Kumar Sharma
- Department
of Chemistry, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Ajmer 305817, India
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7
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Aduriz-Arrizabalaga J, Lopez X, De Sancho D. Atomistic molecular simulations of Aβ-Zn conformational ensembles. Proteins 2024; 92:134-144. [PMID: 37746887 DOI: 10.1002/prot.26590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023]
Abstract
The amyloid-forming Aβ peptide is able to interact with metal cations to form very stable complexes that influence fibril formation and contribute to the onset of Alzheimer's disease. Multiple structures of peptides derived from Aβ in complex with different metals have been resolved experimentally to provide an atomic-level description of the metal-protein interactions. However, Aβ is intrinsically disordered, and hence more amenable to an ensemble description. Molecular dynamics simulations can now reach the timescales needed to generate ensembles for these type of complexes. However, this requires accurate force fields both for the protein and the protein-metal interactions. Here we use state-of-the-art methods to generate force field parameters for the Zn(II) cations in a set of complexes formed by different Aβ variants and combine them with the Amber99SB*-ILDN optimized force field. Upon comparison of NMR experiments with the simulation results, further optimized with a Bayesian/Maximum entropy approach, we provide an accurate description of the molecular ensembles for most Aβ-metal complexes. We find that the resulting conformational ensembles are more heterogeneous than the NMR models deposited in the Protein Data Bank.
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Affiliation(s)
- Julen Aduriz-Arrizabalaga
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), Donostia-San Sebastian, Euskadi, Spain
| | - Xabier Lopez
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), Donostia-San Sebastian, Euskadi, Spain
| | - David De Sancho
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, UPV/EHU & Donostia International Physics Center (DIPC), Donostia-San Sebastian, Euskadi, Spain
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8
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Choi M, Ryu J, Vu HD, Kim D, Youn YJ, Park MH, Huynh PT, Hwang GB, Youn SW, Jeong YH. Transferrin-Conjugated Melittin-Loaded L-Arginine-Coated Iron Oxide Nanoparticles for Mitigating Beta-Amyloid Pathology of the 5XFAD Mouse Brain. Int J Mol Sci 2023; 24:14954. [PMID: 37834402 PMCID: PMC10573775 DOI: 10.3390/ijms241914954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Alzheimer's disease (AD) is one of the most prevalent neurodegenerative diseases and a major contributor to dementia. Although the cause of this condition has been identified long ago as aberrant aggregations of amyloid and tau proteins, effective therapies for it remain elusive. The complexities of drug development for AD treatment are often compounded by the impermeable blood-brain barrier and low-yield brain delivery. In addition, the use of high drug concentrations to overcome this challenge may entail side effects. To address these challenges and enhance the precision of delivery into brain regions affected by amyloid aggregation, we proposed a transferrin-conjugated nanoparticle-based drug delivery system. The transferrin-conjugated melittin-loaded L-arginine-coated iron oxide nanoparticles (Tf-MeLioNs) developed in this study successfully mitigated melittin-induced cytotoxicity and hemolysis in the cell culture system. In the 5XFAD mouse brain, Tf-MeLioNs remarkably reduced amyloid plaque accumulation, particularly in the hippocampus. This study suggested Tf-LioNs as a potential drug delivery platform and Tf-MeLioNs as a candidate for therapeutic drug targeting of amyloid plaques in AD. These findings provide a foundation for further exploration and advancement in AD therapeutics.
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Affiliation(s)
- Moonseok Choi
- Department of Neurodegenerative Diseases Research Group, Korea Brain Research Institute, 61, Cheomdan ro, Dong gu, Daegu 41062, Republic of Korea; (M.C.); (D.K.); (Y.-J.Y.); (G.-B.H.)
| | - Junghwa Ryu
- Department of Radiology, School of Medicine, Daegu Catholic University, 33, Duryugongwon-ro 17-gil, Nam-gu, Daegu 42472, Republic of Korea; (J.R.); (H.D.V.); (M.H.P.); (P.T.H.)
| | - Huy Duc Vu
- Department of Radiology, School of Medicine, Daegu Catholic University, 33, Duryugongwon-ro 17-gil, Nam-gu, Daegu 42472, Republic of Korea; (J.R.); (H.D.V.); (M.H.P.); (P.T.H.)
| | - Dongsoo Kim
- Department of Neurodegenerative Diseases Research Group, Korea Brain Research Institute, 61, Cheomdan ro, Dong gu, Daegu 41062, Republic of Korea; (M.C.); (D.K.); (Y.-J.Y.); (G.-B.H.)
| | - Young-Jin Youn
- Department of Neurodegenerative Diseases Research Group, Korea Brain Research Institute, 61, Cheomdan ro, Dong gu, Daegu 41062, Republic of Korea; (M.C.); (D.K.); (Y.-J.Y.); (G.-B.H.)
| | - Min Hui Park
- Department of Radiology, School of Medicine, Daegu Catholic University, 33, Duryugongwon-ro 17-gil, Nam-gu, Daegu 42472, Republic of Korea; (J.R.); (H.D.V.); (M.H.P.); (P.T.H.)
| | - Phuong Tu Huynh
- Department of Radiology, School of Medicine, Daegu Catholic University, 33, Duryugongwon-ro 17-gil, Nam-gu, Daegu 42472, Republic of Korea; (J.R.); (H.D.V.); (M.H.P.); (P.T.H.)
| | - Gyu-Bin Hwang
- Department of Neurodegenerative Diseases Research Group, Korea Brain Research Institute, 61, Cheomdan ro, Dong gu, Daegu 41062, Republic of Korea; (M.C.); (D.K.); (Y.-J.Y.); (G.-B.H.)
| | - Sung Won Youn
- Department of Radiology, School of Medicine, Daegu Catholic University, 33, Duryugongwon-ro 17-gil, Nam-gu, Daegu 42472, Republic of Korea; (J.R.); (H.D.V.); (M.H.P.); (P.T.H.)
| | - Yun Ha Jeong
- Department of Neurodegenerative Diseases Research Group, Korea Brain Research Institute, 61, Cheomdan ro, Dong gu, Daegu 41062, Republic of Korea; (M.C.); (D.K.); (Y.-J.Y.); (G.-B.H.)
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9
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Yuce-Erarslan E, Domb AAJ, Kasem H, Uversky VN, Coskuner-Weber O. Intrinsically Disordered Synthetic Polymers in Biomedical Applications. Polymers (Basel) 2023; 15:polym15102406. [PMID: 37242981 DOI: 10.3390/polym15102406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/29/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
In biology and medicine, intrinsically disordered synthetic polymers bio-mimicking intrinsically disordered proteins, which lack stable three-dimensional structures, possess high structural/conformational flexibility. They are prone to self-organization and can be extremely useful in various biomedical applications. Among such applications, intrinsically disordered synthetic polymers can have potential usage in drug delivery, organ transplantation, artificial organ design, and immune compatibility. The designing of new syntheses and characterization mechanisms is currently required to provide the lacking intrinsically disordered synthetic polymers for biomedical applications bio-mimicked using intrinsically disordered proteins. Here, we present our strategies for designing intrinsically disordered synthetic polymers for biomedical applications based on bio-mimicking intrinsically disordered proteins.
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Affiliation(s)
- Elif Yuce-Erarslan
- Chemical Engineering, Istanbul University-Cerrahpasa, Avcilar, Istanbul 34320, Turkey
| | - Abraham Avi J Domb
- School of Pharmacy, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Haytam Kasem
- Azrieli College of Engineering, 26 Ya'akov Schreiboim Street, Jerusalem 9103501, Israel
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Orkid Coskuner-Weber
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, No. 106, Beykoz, Istanbul 34820, Turkey
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10
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Puentes-Díaz N, Chaparro D, Morales-Morales D, Flores-Gaspar A, Alí-Torres J. Role of Metal Cations of Copper, Iron, and Aluminum and Multifunctional Ligands in Alzheimer's Disease: Experimental and Computational Insights. ACS OMEGA 2023; 8:4508-4526. [PMID: 36777601 PMCID: PMC9909689 DOI: 10.1021/acsomega.2c06939] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/30/2022] [Indexed: 05/15/2023]
Abstract
Alzheimer's disease (AD) is the most common form of dementia, affecting millions of people around the world. Even though the causes of AD are not completely understood due to its multifactorial nature, some neuropathological hallmarks of its development have been related to the high concentration of some metal cations. These roles include the participation of these metal cations in the production of reactive oxygen species, which have been involved in neuronal damage. In order to avoid the increment in the oxidative stress, multifunctional ligands used to coordinate these metal cations have been proposed as a possible treatment to AD. In this review, we present the recent advances in experimental and computational works aiming to understand the role of two redox active and essential transition-metal cations (Cu and Fe) and one nonbiological metal (Al) and the recent proposals on the development of multifunctional ligands to stop or revert the damaging effects promoted by these metal cations.
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Affiliation(s)
- Nicolás Puentes-Díaz
- Departamento
de Química, Universidad Nacional
de Colombia−Sede Bogotá, Bogotá 11301, Colombia
| | - Diego Chaparro
- Departamento
de Química, Universidad Nacional
de Colombia−Sede Bogotá, Bogotá 11301, Colombia
- Departamento
de Química, Universidad Militar Nueva
Granada, Cajicá 250240, Colombia
| | - David Morales-Morales
- Instituto
de Química, Universidad Nacional Autónoma de México,
Circuito Exterior, Ciudad Universitaria, Ciudad de México 04510, México
| | - Areli Flores-Gaspar
- Departamento
de Química, Universidad Militar Nueva
Granada, Cajicá 250240, Colombia
- Areli Flores-Gaspar − Departamento de Química,
Universidad Militar Nueva
Granada, Cajicá, 250247, Colombia.
| | - Jorge Alí-Torres
- Departamento
de Química, Universidad Nacional
de Colombia−Sede Bogotá, Bogotá 11301, Colombia
- Jorge Alí-Torres − Departamento de Química, Universidad Nacional de
Colombia, Sede Bogotá,11301, Bogotá, Colombia.
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11
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Roldán-Martín L, Sodupe M, Maréchal JD. Computational assessment of the impact of Cu(II) and Al(III) on β-amyloid 42 fibrils: Binding sites, structural stability, and possible physiological implications. Front Neurosci 2023; 17:1110311. [PMID: 36814794 PMCID: PMC9940836 DOI: 10.3389/fnins.2023.1110311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/10/2023] [Indexed: 02/09/2023] Open
Abstract
One of Alzheimer's disease major hallmarks is the aggregation of β-amyloid peptide, a process in which metal ions play an important role. In the present work, an integrative computational study has been performed to identify the metal-binding regions and determine the conformational impact of Cu(II) and Al(III) ion binding to the β-amyloid (Aβ42) fibrillary structure. Through classical and Gaussian accelerated molecular dynamics, it has been observed that the metal-free fiber shows a hinge fan-like motion of the S-shaped structure, maintaining the general conformation. Upon metal coordination, distinctive patterns are observed depending on the metal. Cu(II) binds to the flexible N-terminal region and induces structural changes that could ultimately disrupt the fibrillary structure. In contrast, Al(III) binding takes place with the residues Glu22 and Asp23, and its binding reinforces the core stability of the system. These results give clues on the molecular impact of the interaction of metal ions with the aggregates and sustain their non-innocent roles in the evolution of the illness.
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12
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Conjugates of Tacrine and Salicylic Acid Derivatives as New Promising Multitarget Agents for Alzheimer's Disease. Int J Mol Sci 2023; 24:ijms24032285. [PMID: 36768608 PMCID: PMC9916969 DOI: 10.3390/ijms24032285] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/09/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
A series of previously synthesized conjugates of tacrine and salicylamide was extended by varying the structure of the salicylamide fragment and using salicylic aldehyde to synthesize salicylimine derivatives. The hybrids exhibited broad-spectrum biological activity. All new conjugates were potent inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) with selectivity toward BChE. The structure of the salicylamide moiety exerted little effect on anticholinesterase activity, but AChE inhibition increased with spacer elongation. The most active conjugates were salicylimine derivatives: IC50 values of the lead compound 10c were 0.0826 µM (AChE) and 0.0156 µM (BChE), with weak inhibition of the off-target carboxylesterase. The hybrids were mixed-type reversible inhibitors of both cholinesterases and displayed dual binding to the catalytic and peripheral anionic sites of AChE in molecular docking, which, along with experimental results on propidium iodide displacement, suggested their potential to block AChE-induced β-amyloid aggregation. All conjugates inhibited Aβ42 self-aggregation in the thioflavin test, and inhibition increased with spacer elongation. Salicylimine 10c and salicylamide 5c with (CH2)8 spacers were the lead compounds for inhibiting Aβ42 self-aggregation, which was corroborated by molecular docking to Aβ42. ABTS•+-scavenging activity was highest for salicylamides 5a-c, intermediate for salicylimines 10a-c, low for F-containing salicylamides 7, and non-existent for methoxybenzoylamides 6 and difluoromethoxybenzoylamides 8. In the FRAP antioxidant (AO) assay, the test compounds displayed little or no activity. Quantum chemical analysis and molecular dynamics (MD) simulations with QM/MM potentials explained the AO structure-activity relationships. All conjugates were effective chelators of Cu2+, Fe2+, and Zn2+, with molar compound/metal (Cu2+) ratios of 2:1 (5b) and ~1:1 (10b). Conjugates exerted comparable or lower cytotoxicity than tacrine on mouse hepatocytes and had favorable predicted intestinal absorption and blood-brain barrier permeability. The overall results indicate that the synthesized conjugates are promising new multifunctional agents for the potential treatment of AD.
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da Rosa MM, de Amorim LC, Alves JVDO, Aguiar IFDS, Oliveira FGDS, da Silva MV, dos Santos MTC. The promising role of natural products in Alzheimer's disease. BRAIN DISORDERS 2022. [DOI: 10.1016/j.dscb.2022.100049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
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Mocanu CS, Darie-Ion L, Petre BA, Gradinaru VR, Drochioiu G. A computational study of metal ions interaction with amyloid-β 1-42 peptide structure in hyperpyrexia: Implications for Alzheimer disease. JOURNAL OF KING SAUD UNIVERSITY. SCIENCE 2022; 34:102184. [PMID: 35783243 PMCID: PMC9238029 DOI: 10.1016/j.jksus.2022.102184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 05/28/2023]
Abstract
Given the current context of the SARS-CoV-19 pandemic, among the interfering risky factors with the Aβ peptide aggregation in the brains of Alzheimer's disease (AD) patients can be hyperpyrexia and increased intracranial pressure (ICP). According to our hypothesis on the relationship between hyperpyrexia and cognitive decline in AD, two models of Aβ peptides were used in this study: the structure of AD amyloid beta-peptide and near-atomic resolution fibril structures of the Aβ peptide. Therefore, the binding templates were constructed for Aβ peptide regions able to bind 9 different metal ions. The fragment transformation method was used for the structural comparison between Aβ chains. Molecular dynamics simulation (MDS) was applied using the Nose-Poincare-Anderson equation to generate a theoretically correct NPT (isothermal-isobaric ensemble). The smallest dissimilarities were observed in the case of Cu+ binding potential followed by Co2+, both with similar variation. Structural changes have also occurred as a result of the dynamic simulation. All these changes suggest an aggravating factor in both hyperpyretic and AD conditions. Our findings suggest that elevated temperature and increased intracranial pressure rise the effect of peptide aggregation, by converting α-helix motif to β-sheet and random coil conformation, which are related to the formation of senile plaques in AD brains.
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Affiliation(s)
- Cosmin Stefan Mocanu
- Faculty of Chemistry, "Al. I. Cuza" University of Iasi, 11 Carol I, Iasi 70605, Romania
| | - Laura Darie-Ion
- Faculty of Chemistry, "Al. I. Cuza" University of Iasi, 11 Carol I, Iasi 70605, Romania
| | - Brindusa Alina Petre
- Faculty of Chemistry, "Al. I. Cuza" University of Iasi, 11 Carol I, Iasi 70605, Romania
- Center for Fundamental Research and Experimental Development in Translation Medicine, Regional Institute of Oncology, 2-4 General Henri Mathias Berthelot Str., 700483 Iasi, Romania
| | | | - Gabi Drochioiu
- Faculty of Chemistry, "Al. I. Cuza" University of Iasi, 11 Carol I, Iasi 70605, Romania
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Biological Potential, Gastrointestinal Digestion, Absorption, and Bioavailability of Algae-Derived Compounds with Neuroprotective Activity: A Comprehensive Review. Mar Drugs 2022; 20:md20060362. [PMID: 35736165 PMCID: PMC9227170 DOI: 10.3390/md20060362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 12/04/2022] Open
Abstract
Currently, there is no known cure for neurodegenerative disease. However, the available therapies aim to manage some of the symptoms of the disease. Human neurodegenerative diseases are a heterogeneous group of illnesses characterized by progressive loss of neuronal cells and nervous system dysfunction related to several mechanisms such as protein aggregation, neuroinflammation, oxidative stress, and neurotransmission dysfunction. Neuroprotective compounds are essential in the prevention and management of neurodegenerative diseases. This review will focus on the neurodegeneration mechanisms and the compounds (proteins, polyunsaturated fatty acids (PUFAs), polysaccharides, carotenoids, phycobiliproteins, phenolic compounds, among others) present in seaweeds that have shown in vivo and in vitro neuroprotective activity. Additionally, it will cover the recent findings on the neuroprotective effects of bioactive compounds from macroalgae, with a focus on their biological potential and possible mechanism of action, including microbiota modulation. Furthermore, gastrointestinal digestion, absorption, and bioavailability will be discussed. Moreover, the clinical trials using seaweed-based drugs or extracts to treat neurodegenerative disorders will be presented, showing the real potential and limitations that a specific metabolite or extract may have as a new therapeutic agent considering the recent approval of a seaweed-based drug to treat Alzheimer’s disease.
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Arrigoni F, Di Carlo C, Rovetta A, De Gioia L, Zampella G, Bertini L. Superoxide reduction by Cu‐Amyloid Beta peptide complexes. A Density Functional Theory study. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202200245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Federica Arrigoni
- Università degli Studi di Milano-Bicocca: Universita degli Studi di Milano-Bicocca Biotecnology and Biosciences ITALY
| | - Chiara Di Carlo
- Università degli Studi di Milano-Bicocca: Universita degli Studi di Milano-Bicocca Biotecnology and Biosciences ITALY
| | - Alberto Rovetta
- University of Milano–Bicocca University Library: Universita degli Studi di Milano-Bicocca Biotecnology and Biosciences ITALY
| | - Luca De Gioia
- University of Milan–Bicocca: Universita degli Studi di Milano-Bicocca Biotecnology and Biosciences ITALY
| | - Giuseppe Zampella
- University of Milan–Bicocca: Universita degli Studi di Milano-Bicocca Biotecnology and Biosciences ITALY
| | - Luca Bertini
- Universita' degli studi di MIlano-Bicocca Biotecnologie e Bioscienze Piazza della Scienza 2 20127 Milano ITALY
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Lai C, Chen Z, Ding Y, Chen Q, Su S, Liu H, Ni R, Tang Z. Rapamycin Attenuated Zinc-Induced Tau Phosphorylation and Oxidative Stress in Rats: Involvement of Dual mTOR/p70S6K and Nrf2/HO-1 Pathways. Front Immunol 2022; 13:782434. [PMID: 35197970 PMCID: PMC8858937 DOI: 10.3389/fimmu.2022.782434] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/13/2022] [Indexed: 01/01/2023] Open
Abstract
Alzheimer’s disease is pathologically characterized by abnormal accumulation of amyloid-beta plaques, neurofibrillary tangles, oxidative stress, neuroinflammation, and neurodegeneration. Metal dysregulation, including excessive zinc released by presynaptic neurons, plays an important role in tau pathology and oxidase activation. The activities of mammalian target of rapamycin (mTOR)/ribosomal S6 protein kinase (p70S6K) are elevated in the brains of patients with Alzheimer’s disease. Zinc induces tau hyperphosphorylation via mTOR/P70S6K activation in vitro. However, the involvement of the mTOR/P70S6K pathway in zinc-induced oxidative stress, tau degeneration, and synaptic and cognitive impairment has not been fully elucidated in vivo. Here, we assessed the effect of pathological zinc concentrations in SH-SY5Y cells by using biochemical assays and immunofluorescence staining. Rats (n = 18, male) were laterally ventricularly injected with zinc, treated with rapamycin (intraperitoneal injection) for 1 week, and assessed using the Morris water maze. Evaluation of oxidative stress, tau phosphorylation, and synaptic impairment was performed using the hippocampal tissue of the rats by biochemical assays and immunofluorescence staining. The results from the Morris water maze showed that the capacity of spatial memory was impaired in zinc-treated rats. Zinc sulfate significantly increased the levels of P-mTOR Ser2448, P-p70S6K Thr389, and P-tau Ser356 and decreased the levels of nuclear factor erythroid 2-related factor-2 (Nrf2) and heme oxygenase-1 (HO-1) in SH-SY5Y cells and in zinc-treated rats compared with the control groups. Increased expression of reactive oxygen species was observed in zinc sulfate-induced SH-SY5Y cells and in the hippocampus of zinc-injected rats. Rapamycin, an inhibitor of mTOR, rescued zinc-induced increases in mTOR/p70S6K activation, tau phosphorylation, and oxidative stress, and Nrf2/HO-1 inactivation, cognitive impairment, and synaptic impairment reduced the expression of synapse-related proteins in zinc-injected rats. In conclusion, our findings imply that rapamycin prevents zinc-induced cognitive impairment and protects neurons from tau pathology, oxidative stress, and synaptic impairment by decreasing mTOR/p70S6K hyperactivity and increasing Nrf2/HO-1 activity.
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Affiliation(s)
- Chencen Lai
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, China
- Department of Nosocomial Infection, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Zhuyi Chen
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yuanting Ding
- Department of Nosocomial Infection, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qian Chen
- Department of Nosocomial Infection, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Songbai Su
- Department of Nosocomial Infection, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Heng Liu
- Department of Anesthesiology, Tongren Municipal People’s Hospital, Tongren, China
| | - Ruiqing Ni
- Institute for Regenerative Medicine, University of Zurich, Zurich, Switzerland
- Institute for Biomedical Engineering, Eidgenössische Technische Hochschule Zürich (ETH) and University of Zurich, Zurich, Switzerland
| | - Zhi Tang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, China
- *Correspondence: Zhi Tang,
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Collins AE, Saleh TM, Kalisch BE. Naturally Occurring Antioxidant Therapy in Alzheimer’s Disease. Antioxidants (Basel) 2022; 11:antiox11020213. [PMID: 35204096 PMCID: PMC8868221 DOI: 10.3390/antiox11020213] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 02/06/2023] Open
Abstract
It is estimated that the prevalence rate of Alzheimer’s disease (AD) will double by the year 2040. Although currently available treatments help with symptom management, they do not prevent, delay the progression of, or cure the disease. Interestingly, a shared characteristic of AD and other neurodegenerative diseases and disorders is oxidative stress. Despite profound evidence supporting the role of oxidative stress in the pathogenesis and progression of AD, none of the currently available treatment options address oxidative stress. Recently, attention has been placed on the use of antioxidants to mitigate the effects of oxidative stress in the central nervous system. In preclinical studies utilizing cellular and animal models, natural antioxidants showed therapeutic promise when administered alone or in combination with other compounds. More recently, the concept of combination antioxidant therapy has been explored as a novel approach to preventing and treating neurodegenerative conditions that present with oxidative stress as a contributing factor. In this review, the relationship between oxidative stress and AD pathology and the neuroprotective role of natural antioxidants from natural sources are discussed. Additionally, the therapeutic potential of natural antioxidants as preventatives and/or treatment for AD is examined, with special attention paid to natural antioxidant combinations and conjugates that are currently being investigated in human clinical trials.
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19
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Coskuner-Weber O, Caglayan SI. Secondary structure dependence on simulation techniques and force field parameters: from disordered to ordered proteins. Biophys Rev 2021; 13:1173-1178. [DOI: 10.1007/s12551-021-00850-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022] Open
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Kennedy-Britten OD, Alshammari N, Platts JA. Accelerated Molecular Dynamics to Explore the Binding of Transition Metals to Amyloid-β. ACS Chem Neurosci 2021; 12:4065-4075. [PMID: 34669379 DOI: 10.1021/acschemneuro.1c00466] [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] [Indexed: 01/12/2023] Open
Abstract
We report the accelerated molecular dynamics (aMD) simulation of amyloid-β (Aβ) peptides of four different lengths (16, 28, 40, and 42 residues) and their complexes when bound to Cu(II), Fe(II), or Zn(II). 600 ns equilibrated trajectory data were analyzed for each structure from three independent 200 ns aMD simulations, generating 16 aMD trajectories. We show that the presence of a metal ion leads to reduced size and decreased mobility relative to the free peptide due to the anchoring effect of the ions. The reduced mobility was shown largely to be due to the restricted movement in N-terminal residues, most notably Asp1 and His6 that are involved in the metal-ion coordination in all cases. Significant disruption of the secondary structure and patterns of salt bridge interactions arise on the coordination of metal ions. In this regard, similarities were noted between results for Zn(II) and Fe(II), whereas results for Cu(II) are more comparable to that of the free peptides. Reweighting of free energy surfaces was carried out from aMD data to identify the properties and descriptions of local minima structures.
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Affiliation(s)
| | - Nadiyah Alshammari
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K
| | - James A. Platts
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K
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21
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Al-Shammari N, Savva L, Kennedy-Britten O, Platts JA. Forcefield evaluation and accelerated molecular dynamics simulation of Zn(II) binding to N-terminus of amyloid-β. Comput Biol Chem 2021; 93:107540. [PMID: 34271422 DOI: 10.1016/j.compbiolchem.2021.107540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/11/2021] [Accepted: 06/21/2021] [Indexed: 01/06/2023]
Abstract
We report conventional and accelerated molecular dynamics simulation of Zn(II) bound to the N-terminus of amyloid-β. By comparison against NMR data for the experimentally determined binding mode, we find that certain combinations of forcefield and solvent model perform acceptably in describing the size, shape and secondary structure, and that there is no appreciable difference between implicit and explicit solvent models. We therefore used the combination of ff14SB forcefield and GBSA solvent model to compare the result of different binding modes of Zn(II) to the same peptide, using accelerated MD to enhance sampling and comparing the free peptide simulated in the same way. We show that Zn(II) imparts significant rigidity to the peptide, disrupts the secondary structure and pattern of salt bridges seen in the free peptide, and induces closer contact between residues. Free energy surfaces in 1 or 2 dimensions further highlight the effect of metal coordination on peptide's spatial extent. We also provide evidence that accelerated MD provides improved sampling over conventional MD by visiting as many or more configurations in much shorter simulation times.
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Affiliation(s)
| | - Loizos Savva
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK
| | | | - James A Platts
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
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22
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Asgarshamsi MH, Fassihi A, Hassanzadeh F, Saghaei L, Attar AM, Mohammad-Beigi H. Synthesis, antioxidant activity, and density functional theory study of some novel 4-[(benzo[ d]thiazol-2-ylimino)methyl]phenol derivatives: a comparative approach for the explanation of their radical scavenging activities. Res Pharm Sci 2021; 16:35-47. [PMID: 33953773 PMCID: PMC8074808 DOI: 10.4103/1735-5362.305187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/11/2020] [Accepted: 11/30/2020] [Indexed: 11/25/2022] Open
Abstract
Background and purpose: Radicals produced by Fenton and Haber-Weiss reactions play detrimental roles in our body. Some oxidized proteins as toxic configurations are identified in amyloid-β deposits. These deposits mostly occur in conditions, such as Alzheimer’s disease. Here, we report the synthesis, evaluation of the antioxidant activity, and implementation of density functional theory (DFT) calculations of some4- [(benzo[d]thiazol-2-ylimino) methyl]phenol derivatives. The aim of this study was to provide a comparative theoretical-experimental approach to explain the antioxidant activities of the compounds. Experimental approach: Compounds were synthesized by the reaction between para hydroxybenzaldehyde and aminobenzothiazole derivatives. The scavenging activity of the compounds was evaluated. Various electronic and energetic descriptors such as high occupied molecular orbital and low unoccupied molecular orbital energy gaps, bonding dissociation enthalpy of OH bond, ionization potential, electron affinity, hardness, softness, and spin density of the radical and neutral species were calculated. DFT calculations with B3LYP hybrid functional and 6-311++ G** basis set in the polarizable continuum model were utilized to obtain these descriptors. Findings/Results: Ascorbic acid showed the best DPPH scavenging activity. However, 4d and 4c showed promising antioxidant activity. The values of EHOMO for 4c and 4d were closer to zero, thus, they showed the best scavenging activities. The computational results were in accordance with the experimental ones. The energetic descriptors indicated that the sequential proton loss-electron transfer mechanism is preferred over other mechanisms. Conclusion and implication: Antioxidant activity of 4-[(Benzo[d]thiazol-2-ylimino) methyl]phenol derivatives confirmed by experimental and theoretical documents proves them as novel antioxidants against amyloid-β based disease.
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Affiliation(s)
- Mohammad Hossein Asgarshamsi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Afshin Fassihi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Farshid Hassanzadeh
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Lotfollah Saghaei
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Ahmad Movahedian Attar
- Department of Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Hossein Mohammad-Beigi
- The Centre for Cellular Signal Patterns (CellPAT), Gustav Wieds vej 14, 8000 Aarhus C, Denmark
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Shang N, Zhang L, Wang S, Huang T, Wang Y, Gao X, Xu S, Zhang J, Zhang L, Niu Q, Zhang Q. Increased aluminum and lithium and decreased zinc levels in plasma is related to cognitive impairment in workers at an aluminum factory in China: A cross-sectional study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 214:112110. [PMID: 33677379 DOI: 10.1016/j.ecoenv.2021.112110] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/21/2021] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Previous studies have shown that multiple imbalances of metal ions in the brain are closely associated with the neurodegenerative disorders. Our studies have shown that long-term working exposure to aluminum induces increased plasma aluminum levels and causes cognitive impairment in workers at aluminum factories. OBJECTIVE To explore the levels of nine metals in plasma and the effect on cognitive function among in-service workers. METHODS In this cross-sectional study, cognitive function was assessed using the Montreal Cognitive Assessment (MoCA), which included seven subitems: executive/visuospatial abilities; naming; attention and calculation; language; abstract; recall; and orientation. The plasma levels of nine kinds of metals were measured by inductively coupled plasma-mass spectrometry (ICP-MS). A multivariate generalized linear regression model and Bayesian kernel machine regression (BKMR) were selected to estimate the relationship between metal plasma level and MoCA scores with adjustment for confounders. RESULTS One hundred and eighty-seven workers participated in this study. In the multivariable generalized linear model, among these nine metals studied, five were related to the MoCA score: aluminum, lithium, cobalt, zinc and chromium. In the BKMR model, a significantly negative correlation between the plasma aluminum, lithium and the total MoCA score was observed. Moreover, for subitems on the MoCA scale, the plasma levels of lithium, aluminum, and zinc had a significant correlation with the executive/visuospatial abilities, naming, and orientation abilities, respectively. The log-transformation concentrations of plasma aluminum and lithium were negatively correlated with the executive/visuospatial abilities and naming abilities, respectively. The log-transformation plasma zinc concentration was positively correlated with orientation abilities. CONCLUSION Based on the results, we determined that increased aluminum and lithium and decreased zinc levels in plasma were associated with the incidence of mild cognitive impairment (MCI) in workers at a Chinese aluminum plant.
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Affiliation(s)
- Nan Shang
- Department of Pharmacy, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China; Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Lan Zhang
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Shuo Wang
- Department of Physical and Chemical, Beijing Chaoyang District Center for Disease Control and Prevention, Beijing 100021, China
| | - Tao Huang
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Yanhong Wang
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Xiaocheng Gao
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Shimeng Xu
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Jingqi Zhang
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Ling Zhang
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Qiao Niu
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Qinli Zhang
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi 030001, China.
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Zhen Y, Chen L, Ma X, Ding G, Zhang D, Chen Q. β-Amyloid Peptide 1-42-Conjugated Magnetic Nanoparticles for the Isolation and Purification of Glycoproteins in Egg White. ACS APPLIED MATERIALS & INTERFACES 2021; 13:14028-14036. [PMID: 33730480 DOI: 10.1021/acsami.1c02356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Aβ1-42-conjugated magnetic nanoparticles, Aβ1-42@MNP, were prepared by covalently coupling Aβ1-42 to hyperbranched polyethyleneimine (PEI)-modified magnetic nanoparticles via N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDC). Aβ1-42's high binding capacity to glycosyl groups facilitates Aβ1-42@MNP composite to be a promising selective adsorbent for glycoproteins in egg whites. In our study, under conditions of pH 4.0, the adsorption efficiency of Aβ1-42@MNP composite for ovalbumin (100 μg mL-1) was 98.4% and its maximum adsorption capacity was 344.8 mg g -1; under the condition of pH 4.0 and 200 mmol L-1 NaCl, its adsorption efficiencies for ovalbumin and ovotransferrin were 96.9% and 60.0%, respectively. According to these primary data, in practice, ovalbumin was removed from egg white by Aβ1-42@MNP composite at pH 4.0 (step I), and then after adding NaCl until the final salt concentration reached 200 mmol L-1 (pretreated egg white), we utilized the same adsorbent to further isolate/purify glycoproteins (step II). SDS-PAGE results showed that Aβ1-42@MNP composite could largely remove ovalbumin in step I and could isolate/purify the remaining ovalbumin and ovotransferrin in step II. LC-MS/MS analysis results showed that the removal of ovalbumin reduced its percentage in egg white samples from 32.93% to 11.05% in step I and the remaining ovalbumin and ovotransferrin were enriched in step II, where the final percentage reached 11.6% and 12.6%, respectively. In summary, 81 protein species were identified after two-step extraction with Aβ1-42@MNP on egg white, while only 46 protein species were identified directly from raw egg white without any pretreatment. This work well illustrates the excellent adsorption performance of Aβ1-42@MNP composite to glycoproteins and its potential in the application of proteomic studies on low-abundance proteins in egg white.
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Affiliation(s)
- Yi Zhen
- Institute of Translational Medicine, Department of Pharmacy, Shenyang Medical College, Shenyang 110034, China
| | - Lei Chen
- Institute of Translational Medicine, Department of Pharmacy, Shenyang Medical College, Shenyang 110034, China
| | - Xiaoyi Ma
- Institute of Translational Medicine, Department of Pharmacy, Shenyang Medical College, Shenyang 110034, China
| | - Guoyu Ding
- Institute of Translational Medicine, Department of Pharmacy, Shenyang Medical College, Shenyang 110034, China
| | - Dandan Zhang
- Institute of Translational Medicine, Department of Pharmacy, Shenyang Medical College, Shenyang 110034, China
| | - Qing Chen
- Institute of Translational Medicine, Department of Pharmacy, Shenyang Medical College, Shenyang 110034, China
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Barbosa ED, Neto JXL, Teixeira DG, Bezerra KS, do Amaral VS, Oliveira JIN, Lima JPMS, Machado LD, Fulco UL. Exploring human porphobilinogen synthase metalloprotein by quantum biochemistry and evolutionary methods. Metallomics 2021; 13:6206860. [PMID: 33791795 DOI: 10.1093/mtomcs/mfab017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/16/2021] [Accepted: 03/21/2021] [Indexed: 12/16/2022]
Abstract
Previous studies have shown the porphobilinogen synthase (PBGS) zinc-binding mechanism and its conservation among the living cells. However, the precise molecular interaction of zinc with the active center of the enzyme is unknown. In particular, quantum chemistry techniques within the density functional theory (DFT) framework have been the key methodology to describe metalloproteins, when one is looking for a compromise between accuracy and computational feasibility. Considering this, we used DFT-based models within the molecular fractionation with conjugate caps scheme to evaluate the binding energy features of zinc interacting with the human PBGS. Besides, phylogenetic and clustering analyses were successfully employed in extracting useful information from protein sequences to identify groups of conserved residues that build the ions-binding site. Our results also report a conservative assessment of the relevant amino acids, as well as the benchmark analysis of the calculation models used. The most relevant intermolecular interactions in Zn2+-PBGS are due to the amino acids CYS0122, CYS0124, CYS0132, ASP0169, SER0168, ARG0221, HIS0131, ASP0120, GLY0133, VAL0121, ARG0209, and ARG0174. Among these residues, we highlighted ASP0120, GLY0133, HIS0131, SER0168, and ARG0209 by co-occurring in all clusters generated by unsupervised clustering analysis. On the other hand, the triple cysteines at 2.5 Å from zinc (CYS0122, CYS0124, and CYS0132) have the highest energy attraction and are absent in the taxa Viridiplantae, Sar, Rhodophyta, and some Bacteria. Additionally, the performance of the DFT-based models shows that the processing time-dependence is more associated with the choice of the basis set than the exchange-correlation functional.
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Affiliation(s)
- E D Barbosa
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - J X Lima Neto
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - D G Teixeira
- Institute of Tropical Medicine, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - K S Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - V S do Amaral
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - J I N Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - J P M Santos Lima
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - L D Machado
- Departamento de Física Teórica e Experimental, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - U L Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
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Manna SL, Florio D, Iacobucci I, Napolitano F, Benedictis ID, Malfitano AM, Monti M, Ravera M, Gabano E, Marasco D. A Comparative Study of the Effects of Platinum (II) Complexes on β-Amyloid Aggregation: Potential Neurodrug Applications. Int J Mol Sci 2021; 22:ijms22063015. [PMID: 33809522 PMCID: PMC7998721 DOI: 10.3390/ijms22063015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 01/21/2023] Open
Abstract
Herein the effects of three platinum complexes, namely (SP-4-2)-(2,2'-bipyridine)dichloridoplatinum(II), Pt-bpy, (SP-4-2)-dichlorido(1,10-phenanthroline) platinum(II), Pt-phen, and (SP-4-2)-chlorido(2,2':6',2''-terpyridine)platinum(II) chloride, Pt-terpy, on the aggregation of an amyloid model system derived from the C-terminal domain of Aβ peptide (Aβ21-40) were investigated. Thioflavin T (ThT) binding assays revealed the ability of Pt(II) compounds to repress amyloid aggregation in a dose-dependent way, whereas the ability of Aβ21-40 peptide to interfere with ligand field of metal complexes was analyzed through UV-Vis absorption spectroscopy and electrospray ionization mass spectrometry. Spectroscopic data provided micromolar EC50 values and allowed to assess that the observed inhibition of amyloid aggregation is due to the formation of adducts between Aβ21-40 peptide and complexes upon the release of labile ligands as chloride and that they can explore different modes of coordination toward Aβ21-40 with respect to the entire Aβ1-40 polypeptide. In addition, conformational studies through circular dichroism (CD) spectroscopy suggested that Pt-terpy induces soluble β-structures of monomeric Aβ21-40, thus limiting self-recognition. Noticeably, Pt-terpy demonstrated the ability to reduce the cytotoxicity of amyloid peptide in human SH-SY5Y neuroblastoma cells. Presented data corroborate the hypothesis to enlarge the application field of already known metal-based agents to neurodegenerative diseases, as potential neurodrugs.
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Affiliation(s)
- Sara La Manna
- Department of Pharmacy, University of Naples “Federico II”, 80131 Naples, Italy; (S.L.M.); (D.F.); (I.D.B.)
| | - Daniele Florio
- Department of Pharmacy, University of Naples “Federico II”, 80131 Naples, Italy; (S.L.M.); (D.F.); (I.D.B.)
| | - Ilaria Iacobucci
- Department of Chemical Sciences, CEINGE Biotecnologie Avanzate S.c.a r.l., “University of Naples Federico II”, 80131 Naples, Italy; (I.I.); (M.M.)
| | - Fabiana Napolitano
- Department of Translational Medical Science, University of Naples “Federico II”, 80131 Naples, Italy; (F.N.); (A.M.M.)
| | - Ilaria De Benedictis
- Department of Pharmacy, University of Naples “Federico II”, 80131 Naples, Italy; (S.L.M.); (D.F.); (I.D.B.)
| | - Anna Maria Malfitano
- Department of Translational Medical Science, University of Naples “Federico II”, 80131 Naples, Italy; (F.N.); (A.M.M.)
| | - Maria Monti
- Department of Chemical Sciences, CEINGE Biotecnologie Avanzate S.c.a r.l., “University of Naples Federico II”, 80131 Naples, Italy; (I.I.); (M.M.)
| | - Mauro Ravera
- Department of Sciences and Technological Innovation (DiSIT), University of Piemonte Orientale “A. Avogadro”, 15121 Alessandria, Italy; (M.R.); (E.G.)
| | - Elisabetta Gabano
- Department of Sciences and Technological Innovation (DiSIT), University of Piemonte Orientale “A. Avogadro”, 15121 Alessandria, Italy; (M.R.); (E.G.)
| | - Daniela Marasco
- Department of Pharmacy, University of Naples “Federico II”, 80131 Naples, Italy; (S.L.M.); (D.F.); (I.D.B.)
- Correspondence: ; Tel.: +39-081-2534512; Fax: +39-081-2534574
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27
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Liu C, Luo X. Potential molecular and graphene oxide chelators to dissolve amyloid-β plaques in Alzheimer's disease: a density functional theory study. J Mater Chem B 2021; 9:2736-2746. [PMID: 33688880 DOI: 10.1039/d0tb02985h] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The onset of Alzheimer's disease (AD) is caused by amyloid-β (Aβ) aggregation. Elevated levels of metals, specifically copper, zinc, iron, and aluminum, accumulate in senile Aβ; plaque deposits, disrupting normal brain homeostasis and cognitive functions. In this investigation, we studied the potential of several molecular and graphene oxide chelators to be used for future AD research and chelation therapy. To understand the interactions between selected metals (Cu, Zn, Fe, and Al), the Aβ peptide, and various potential metal chelating compounds, we implemented the density functional theory (DFT) method to calculate the binding energies of each metal-molecule complex. The binding energy of each metal-chelator complex was compared with that of the metal-Aβ compound to determine the chelation potential of the selected chelator. The potential chelating agents studied were 8-hydroxyquinoline-2-carboxaldehyde isonicotinoyl hydrazone (INNHQ), 8-hydroxyquinoline-2-carboxaldehyde 2-furoyl hydrazone (HQFUH), quercetin, and graphene oxide (GO). Our calculated binding energies revealed that the HQFUH molecule holds direct ability to chelate copper, zinc, iron, and aluminum. In addition, the GO complex with a 12.5% oxygen concentration demonstrates aluminum chelation ability. Our results demonstrate that HQFUH and GO can be used in future AD drug development research and therapy to target toxic metal-Aβ interactions and reduce Aβ aggregation.
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Affiliation(s)
- Christina Liu
- National Graphene Research and Development Center, Springfield, Virginia 22151, USA.
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28
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Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev 2021; 121:2545-2647. [PMID: 33543942 PMCID: PMC8836097 DOI: 10.1021/acs.chemrev.0c01122] [Citation(s) in RCA: 368] [Impact Index Per Article: 122.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Peter Faller
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
- Molecular Biology, University of Naples Federico II, Naples 80138, Italy
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saeed Najafi
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Applied Sciences, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Mara Chiricotto
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - James McCarty
- Chemistry Department, Western Washington University, Bellingham, Washington 98225, United States
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Carol Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yifat Miller
- Department of Chemistry and The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | | | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Stepan Timr
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Jiaxing Chen
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Brianna Hnath
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, and Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Sylvain Lesné
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Science, Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Fabio Sterpone
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Andrew J Doig
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, U.K
| | - Philippe Derreumaux
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
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29
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Babu E, Bhuvaneswari J, Rajakumar K, Sathish V, Thanasekaran P. Non-conventional photoactive transition metal complexes that mediated sensing and inhibition of amyloidogenic aggregates. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213612] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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30
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Akbayrak IY, Caglayan SI, Ozcan Z, Uversky VN, Coskuner-Weber O. Current Challenges and Limitations in the Studies of Intrinsically Disordered Proteins in Neurodegenerative Diseases by Computer Simulations. Curr Alzheimer Res 2020; 17:805-818. [PMID: 33167839 DOI: 10.2174/1567205017666201109094908] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 10/06/2020] [Accepted: 10/13/2020] [Indexed: 11/22/2022]
Abstract
Experiments face challenges in the analysis of intrinsically disordered proteins in solution due to fast conformational changes and enhanced aggregation propensity. Computational studies complement experiments, being widely used in the analyses of intrinsically disordered proteins, especially those positioned at the centers of neurodegenerative diseases. However, recent investigations - including our own - revealed that computer simulations face significant challenges and limitations themselves. In this review, we introduced and discussed some of the scientific challenges and limitations of computational studies conducted on intrinsically disordered proteins. We also outlined the importance of future developments in the areas of computational chemistry and computational physics that would be needed for generating more accurate data for intrinsically disordered proteins from computer simulations. Additional theoretical strategies that can be developed are discussed herein.
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Affiliation(s)
- Ibrahim Y Akbayrak
- Materials Science and Technologies, Turkish-German University, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Turkey
| | - Sule I Caglayan
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Turkey
| | - Zilan Ozcan
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Turkey
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, United States
| | - Orkid Coskuner-Weber
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Turkey
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31
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Arrigoni F, Rizza F, Tisi R, De Gioia L, Zampella G, Bertini L. On the propagation of the OH radical produced by Cu-amyloid beta peptide model complexes. Insight from molecular modelling. Metallomics 2020; 12:1765-1780. [PMID: 33052996 DOI: 10.1039/d0mt00113a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Oxidative stress and metal dyshomeostasis are considered as crucial factors in the pathogenesis of Alzheimer's disease (AD). Indeed, transition metal ions such as Cu(ii) can generate Reactive Oxygen Species (ROS) via O2 Fenton-like reduction, catalyzed by Cu(ii) coordinated to the Amyloid beta (Aβ) peptide. Despite intensive effort, the mechanisms of ROS-induced molecular damage remain poorly understood. In the present paper, we investigate on the basis of molecular modelling computations the mechanism of OH radical propagation toward the Aβ peptide, starting from the end-product of OH radical generation by Cu(ii)·Aβ. We evaluate (i) the OH oxidative capacity, as well as the energetics of the possible Aβ oxidation target residues, by quantum chemistry Density Functional Theory (DFT) on coordination models of Cu(ii)/OH/Aβ and (ii) the motion of the OH˙ approaching the Aβ target residues by classical Molecular Dynamics (MD) on the full peptide Cu(ii)/OH/Aβ(1-16). The results show that the oxidative capacity of OH coordinated Cu(ii)Aβ is significantly lower than that of the free OH radical and that propagation toward Aβ Asp and His residues is favoured over Tyr residues. These results are discussed on the basis of the recent literature on in vitro Aβ metal-catalyzed oxidation and on the possible implications for the AD oxidative stress mechanism.
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Affiliation(s)
- Federica Arrigoni
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
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32
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Ali AM, Kunugi H. Royal Jelly as an Intelligent Anti-Aging Agent-A Focus on Cognitive Aging and Alzheimer's Disease: A Review. Antioxidants (Basel) 2020; 9:E937. [PMID: 33003559 PMCID: PMC7601550 DOI: 10.3390/antiox9100937] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/24/2020] [Accepted: 09/24/2020] [Indexed: 02/08/2023] Open
Abstract
The astronomical increase of the world's aged population is associated with the increased prevalence of neurodegenerative diseases, heightened disability, and extremely high costs of care. Alzheimer's Disease (AD) is a widespread, age-related, multifactorial neurodegenerative disease that has enormous social and financial drawbacks worldwide. The unsatisfactory outcomes of available AD pharmacotherapy necessitate the search for alternative natural resources that can target various the underlying mechanisms of AD pathology and reduce disease occurrence and/or progression. Royal jelly (RJ) is the main food of bee queens; it contributes to their fertility, long lifespan, and memory performance. It represents a potent nutraceutical with various pharmacological properties, and has been used in a number of preclinical studies to target AD and age-related cognitive deterioration. To understand the mechanisms through which RJ affects cognitive performance both in natural aging and AD, we reviewed the literature, elaborating on the metabolic, molecular, and cellular mechanisms that mediate its anti-AD effects. Preclinical findings revealed that RJ acts as a multidomain cognitive enhancer that can restore cognitive performance in aged and AD models. It promotes brain cell survival and function by targeting multiple adversities in the neuronal microenvironment such as inflammation, oxidative stress, mitochondrial alterations, impaired proteostasis, amyloid-β toxicity, Ca excitotoxicity, and bioenergetic challenges. Human trials using RJ in AD are limited in quantity and quality. Here, the limitations of RJ-based treatment strategies are discussed, and directions for future studies examining the effect of RJ in cognitively impaired subjects are noted.
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Affiliation(s)
- Amira Mohammed Ali
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-0031, Japan;
- Department of Psychiatric Nursing and Mental Health, Faculty of Nursing, Alexandria University, Alexandria 21527, Egypt
| | - Hiroshi Kunugi
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-0031, Japan;
- Department of Psychiatry, Teikyo University School of Medicine, Tokyo 173-8605, Japan
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33
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Boopathi S, Dinh Quoc Huy P, Gonzalez W, Theodorakis PE, Li MS. Zinc binding promotes greater hydrophobicity inAlzheimer's Aβ42peptide than copper binding: Molecular dynamics and solvation thermodynamics studies. Proteins 2020; 88:1285-1302. [DOI: 10.1002/prot.25901] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/04/2020] [Accepted: 05/13/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Subramanian Boopathi
- Centro de Bioinformática y Simulación Molecular (CBSM), Facultad de IngenieríaUniversidad de Talca Talca Chile
| | | | - Wendy Gonzalez
- Centro de Bioinformática y Simulación Molecular (CBSM), Facultad de IngenieríaUniversidad de Talca Talca Chile
- Millennium Nucleus of Ion Channels‐Associated Diseases (MiNICAD)Universidad de Talca Talca Chile
| | | | - Mai Suan Li
- Institute of PhysicsPolish Academy of Sciences Warsaw Poland
- Institute for Computational Science and Technology, Quang Trung Software City Tan Chanh Hiep Ward Ho Chi Minh City Vietnam
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34
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Saini RK, Thakur H, Goyal B. Effect of Piedmont mutation (L34V) on the structure, dynamics, and aggregation of Alzheimer's Aβ 40 peptide. J Mol Graph Model 2020; 97:107571. [PMID: 32143150 DOI: 10.1016/j.jmgm.2020.107571] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/26/2020] [Accepted: 02/19/2020] [Indexed: 12/22/2022]
Abstract
The amyloid-β (Aβ) aggregation in the brain has been associated with the development of Alzheimer's disease (AD). The previous studies have reported that Piedmont mutation (L34V) increases the rate of Aβ40 aggregation. However, the underlying molecular mechanism of the effect of L34V mutation on Aβ40 structure, dynamics, and aggregation remains largely unclear. In the present study, molecular dynamics (MD) simulations were performed to elucidate the effect of L34V mutation on the structural changes and conformational dynamics of Aβ40. The secondary structure analysis highlight that L34V mutation enhances Aβ40 self-assembly due to the formation of aggregation-prone β-sheet structure at the C-terminus of Aβ40 monomeric structure. The higher probability of Asp23-Lys28 salt bridge interaction in Aβ40(L34V) leads to aggregation prone β-sheet conformations, which has the potential to increase the fibril formation rate. The free energy landscape (FEL) analysis depict a sampling of coil conformation in the free energy minima of Aβ40, whereas the aggregation-prone β-sheet conformation was observed at the C-terminal region of Aβ40(L34V) in the minimum energy conformations extracted from FEL of Aβ40(L34V). MD simulations, in agreement with experiment, highlight that L34V mutation increases Aβ40 aggregation as the sampling of the aggregation-prone β-sheet conformation substantially increased. Overall, MD simulations provided atomic level details into the increased fibril formation tendency upon L34V mutation and physical insights into the L34V-mediated conformational as well as structural changes in Aβ40.
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Affiliation(s)
- Rajneet Kaur Saini
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, 140406, Punjab, India
| | - Hema Thakur
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India.
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35
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Yan Q, Liu W, Wen H, Zhibin X, Meng Z. A New Fluorescent Sensor for Fe
3+
Based on Glycoluril Molecular Clip. ChemistrySelect 2020. [DOI: 10.1002/slct.201904902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Qiaoli Yan
- School of Chemistry and Chemical Engineering Beijing Institute of Technology Institution 5 South Zhongguancun Street Beijing 100081 P.R. China
| | - Wenjin Liu
- School of Chemistry and Chemical Engineering Beijing Institute of Technology Institution 5 South Zhongguancun Street Beijing 100081 P.R. China
| | - Hongliang Wen
- School of Chemistry and Chemical Engineering Beijing Institute of Technology Institution 5 South Zhongguancun Street Beijing 100081 P.R. China
| | - Xu Zhibin
- School of Chemistry and Chemical Engineering Beijing Institute of Technology Institution 5 South Zhongguancun Street Beijing 100081 P.R. China
| | - Zihui Meng
- School of Chemistry and Chemical Engineering Beijing Institute of Technology Institution 5 South Zhongguancun Street Beijing 100081 P.R. China
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Platts JA. Quantum chemical molecular dynamics and metadynamics simulation of aluminium binding to amyloid-β and related peptides. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191562. [PMID: 32257321 PMCID: PMC7062105 DOI: 10.1098/rsos.191562] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/10/2019] [Indexed: 06/11/2023]
Abstract
We report semi-empirical tight-binding simulations of the interaction between Al(III) and biologically relevant peptides. The GFN2-XTB method is shown to accurately reproduce previously reported and density functional theory (DFT)-calculated geometries of model systems. Molecular dynamics simulations based on this method are able to sample peptide flexibility over timescales of up to nanoseconds, but these timescales are insufficient to explore potential changes in metal-peptide binding modes. To achieve this, metadynamics simulations using root mean square deviation as a collective variable were employed. With suitably chosen biasing potentials, these are able to efficiently explore diverse coordination modes, for instance, through Glu and/or Asp residues in a model peptide. Using these methods, we find that Al(III) binding to the N-terminal sequence of amyloid-β is highly fluxional, with all acidic sidechains and several backbone oxygens participating in coordination. We also show that such simulations could provide a means to predict a priori possible binding modes as a precursor to longer, atomistic simulations.
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Singh R, Mishra NK, Singh N, Rawal P, Gupta P, Joshi KB. Transition metal ions induced secondary structural transformation in a hydrophobized short peptide amphiphile. NEW J CHEM 2020. [DOI: 10.1039/d0nj01501f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transition metal ions mediate the secondary structural transformation of hydrophobized sPA and can be applied to the design and development of stimuli-responsive nanomaterials.
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Affiliation(s)
- Ramesh Singh
- Department of Chemistry
- School of Chemical Science and Technology
- Dr Harisingh Gour Central University
- Sagar
- India
| | | | - Narendra Singh
- Department of Chemistry
- Indian Institute of Technology
- Kanpur
- India
| | - Parveen Rawal
- Department of Chemistry
- Indian Institute of Technology
- Roorkee 247667
- India
| | - Puneet Gupta
- Department of Chemistry
- Indian Institute of Technology
- Roorkee 247667
- India
| | - Khashti Ballabh Joshi
- Department of Chemistry
- School of Chemical Science and Technology
- Dr Harisingh Gour Central University
- Sagar
- India
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Owen MC, Gnutt D, Gao M, Wärmländer SKTS, Jarvet J, Gräslund A, Winter R, Ebbinghaus S, Strodel B. Effects of in vivo conditions on amyloid aggregation. Chem Soc Rev 2019; 48:3946-3996. [PMID: 31192324 DOI: 10.1039/c8cs00034d] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
One of the grand challenges of biophysical chemistry is to understand the principles that govern protein misfolding and aggregation, which is a highly complex process that is sensitive to initial conditions, operates on a huge range of length- and timescales, and has products that range from protein dimers to macroscopic amyloid fibrils. Aberrant aggregation is associated with more than 25 diseases, which include Alzheimer's, Parkinson's, Huntington's, and type II diabetes. Amyloid aggregation has been extensively studied in the test tube, therefore under conditions that are far from physiological relevance. Hence, there is dire need to extend these investigations to in vivo conditions where amyloid formation is affected by a myriad of biochemical interactions. As a hallmark of neurodegenerative diseases, these interactions need to be understood in detail to develop novel therapeutic interventions, as millions of people globally suffer from neurodegenerative disorders and type II diabetes. The aim of this review is to document the progress in the research on amyloid formation from a physicochemical perspective with a special focus on the physiological factors influencing the aggregation of the amyloid-β peptide, the islet amyloid polypeptide, α-synuclein, and the hungingtin protein.
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Affiliation(s)
- Michael C Owen
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - David Gnutt
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany and Lead Discovery Wuppertal, Bayer AG, 42096 Wuppertal, Germany
| | - Mimi Gao
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 4a, 44227 Dortmund, Germany and Sanofi-Aventis Deutschland GmbH, R&D, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Sebastian K T S Wärmländer
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Jüri Jarvet
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 4a, 44227 Dortmund, Germany
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, 42525 Jülich, Germany. and Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
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Turner M, Mutter ST, Kennedy-Britten OD, Platts JA. Molecular dynamics simulation of aluminium binding to amyloid-β and its effect on peptide structure. PLoS One 2019; 14:e0217992. [PMID: 31185053 PMCID: PMC6559712 DOI: 10.1371/journal.pone.0217992] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/23/2019] [Indexed: 01/05/2023] Open
Abstract
Multiple microsecond-length molecular dynamics simulations of complexes of Al(III) with amyloid-β (Aβ) peptides of varying length are reported, employing a non-bonded model of Al-coordination to the peptide, which is modelled using the AMBER ff14SB forcefield. Individual simulations reach equilibrium within 100 to 400 ns, as determined by root mean square deviations, leading to between 2.1 and 2.7 μs of equilibrated data. These reveal a compact set of configurations, with radius of gyration similar to that of the metal free peptide but larger than complexes with Cu, Fe and Zn. Strong coordination through acidic residues Glu3, Asp7 and Glu11 is maintained throughout all trajectories, leading to average coordination numbers of approximately 4 to 5. Helical conformations predominate, particularly in the longer Al-Aβ40 and Al-Aβ42 peptides, while β-strand forms are rare. Binding of the small, highly charged Al(III) ion to acidic residues in the N-terminus strongly disrupts their ability to engage in salt bridges, whereas residues outside the metal binding region engage in salt bridges to similar extent to the metal-free peptide, including the Asp23-Lys28 bridge known to be important for formation of fibrils. High helical content and disruption of salt bridges leads to characteristic tertiary structure, as shown by heat maps of contact between residues as well as representative clusters of trajectories.
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Affiliation(s)
- Matthew Turner
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom
| | - Shaun T. Mutter
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom
| | | | - James A. Platts
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom
- * E-mail:
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Wahab HA, Amaro RE, Cournia Z. A Celebration of Women in Computational Chemistry. J Chem Inf Model 2019; 59:1683-1692. [DOI: 10.1021/acs.jcim.9b00368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, 3234 Urey Hall, #0340, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
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