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Martín LR, Santiago LR, Korendovych IV, Sodupe M, Maréchal JD. Computational modelling of supramolecular metallopeptide assemblies. Methods Enzymol 2024; 697:211-245. [PMID: 38816124 DOI: 10.1016/bs.mie.2024.03.021] [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: 06/01/2024]
Abstract
Among the important questions in supramolecular peptide self-assemblies are their interactions with metallic compounds and ions. In the last decade, intensive efforts have been devoted to understanding the structural properties of these interactions including their dynamical and catalytic impact in natural and de novo systems. Since structural insights from experimental approaches could be particularly challenging, computational chemistry methods are interesting complementary tools. Here, we present the general multiscale strategies we developed and applied for the study of metallopeptide assemblies. These strategies include prediction of metal binding site, docking of metallic moieties, classical and accelerated molecular dynamics and finally QM/MM calculations. The systems of choice for this chapter are, on one side, peptides involved in neurodegenerative diseases and, on the other, de novo fibrillar systems with catalytic properties. Both successes and remaining challenges are highlighted so that the protocol could be apply to other system of this kind.
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Affiliation(s)
| | | | - Ivan V Korendovych
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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2
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Roldán-Martín L, Sodupe M, Maréchal JD. Computational Study of Amyloidβ 42 Familial Mutations and Metal Interaction: Impact on Monomers and Aggregates Dynamical Behaviors. Inorg Chem 2024; 63:4725-4737. [PMID: 38408469 PMCID: PMC10934806 DOI: 10.1021/acs.inorgchem.3c04555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/28/2024]
Abstract
One of the main hallmarks of Alzheimer's Disease is the formation of β-amyloid plaques, whose formation may be enhanced by metal binding or the appearance of familial mutations. In the present study, the simultaneous effect of familial mutations (E22Q, E22G, E22K, and D23N) and binding to metal ions (Cu(II) or Al(III)) is studied at the Aβ42 monomeric and fibrillar levels. With the application of GaMD and MD simulations, it is observed that the effects of metal binding and mutations differ in the monomeric and fibrillar forms. In the monomeric structures, without metal binding, all mutations reduce the amount of α-helix and increase, in some cases, the β-sheet content. In the presence of Cu(II) and Al(III) metal ions, the peptide becomes less flexible, and the β-sheet content decreases in favor of forming α-helix motifs that stabilize the system through interhelical contacts. Regarding the fibrillar structures, mutations decrease the opening of the fiber in the vertical axis, thereby stabilizing the S-shaped structure of the fiber. This effect is, in general, enhanced upon metal binding. These results may explain the different Aβ42 aggregation patterns observed in familial mutations.
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Affiliation(s)
- Lorena Roldán-Martín
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Spain
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola
del Vallès, Spain
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3
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Krupa P, La Penna G, Li MS. Amyloid- β Tetramers and Divalent Cations at the Membrane/Water Interface: Simple Models Support a Functional Role. Int J Mol Sci 2023; 24:12698. [PMID: 37628878 PMCID: PMC10454299 DOI: 10.3390/ijms241612698] [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: 06/30/2023] [Revised: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Charge polarization at the membrane interface is a fundamental process in biology. Despite the lower concentration compared to the abundant monovalent ions, the relative abundance of divalent cations (Ca2+, Mg2+, Zn2+, Fe2+, Cu2+) in particular spaces, such as the neuron synapse, raised many questions on the possible effects of free multivalent ions and of the required protection of membranes by the eventual defects caused by the free forms of the cations. In this work, we first applied a recent realistic model of divalent cations to a well-investigated model of a polar lipid bilayer, di-myristoyl phosphatidyl choline (DMPC). The full atomistic model allows a fairly good description of changes in the hydration of charged and polar groups upon the association of cations to lipid atoms. The lipid-bound configurations were analyzed in detail. In parallel, amyloid-β 1-42 (Aβ42) peptides assembled into tetramers were modeled at the surface of the same bilayer. Two of the protein tetramers' models were loaded with four Cu2+ ions, the latter bound as in DMPC-free Aβ42 oligomers. The two Cu-bound models differ in the binding topology: one with each Cu ion binding each of the monomers in the tetramer; one with pairs of Cu ions linking two monomers into dimers, forming tetramers as dimers of dimers. The models here described provide hints on the possible role of Cu ions in synaptic plasticity and of Aβ42 oligomers in storing the same ions away from lipids. The release of structurally disordered peptides in the synapse can be a mechanism to recover ion homeostasis and lipid membranes from changes in the divalent cation concentration.
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Affiliation(s)
- Pawel Krupa
- Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland; (P.K.); (M.S.L.)
| | - Giovanni La Penna
- Institute of Chemistry of Organometallic Compounds, National Research Council, 50019 Sesto Fiorentino, Italy
- Section of Roma Tor Vergata, National Institute of Nuclear Physics, 00133 Roma, Italy
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland; (P.K.); (M.S.L.)
- Institute for Computational Science and Technology, Ho Chi Minh City 700000, Vietnam
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Gupta S, Dasmahapatra AK. Enhanced stability of a disaggregated Aβ fibril on removal of ligand inhibits refibrillation: An all atom Molecular Dynamics simulation study. Int J Biol Macromol 2023; 240:124481. [PMID: 37076062 DOI: 10.1016/j.ijbiomac.2023.124481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
The extraneuronally deposited senile plaques, composed of neurotoxic aggregates of Aβ fibril, define Alzheimer's disease (AD). Natural compounds have been tested for their destabilization potential on Aβ fibril, thereby curing AD. However, the resultant destabilized Aβ fibril, needs to be checked for its irreversibility to the native organized state after removal of the ligand. Herein, we assessed the stability of a destabilized fibril after the ligand (ellagic acid represented as REF) is removed from the complex. The study has been conducted via Molecular Dynamics (MD) simulation of 1 μs for both Aβ-Water (control) and Aβ-REF″ (test or REF removed) system. The increased value of RMSD, Rg, SASA, lower β-sheet content and reduced number of H-bonds explains enhanced destabilization observed in Aβ-REF″ system. The increased inter-chain distance demonstrates breaking of the residual contacts, testifying the drift of terminal chains from the pentamer. The increased SASA along with the ∆Gps(polar solvation energy) accounts for the reduced interaction amongst residues, and more with solvent molecules, governing irreversibility to native state. The higher Gibb's free energy of the misaligned structure of Aβ-REF″ ensures irreversibility to the organized structure due to its inability to cross such high energy barrier. The observed stability of the disaggregated structure, despite ligand elimination, establishes the effectiveness of the destabilization technique as a promising therapeutic approach towards treating AD.
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Affiliation(s)
- Shivani Gupta
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ashok Kumar Dasmahapatra
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India; Center for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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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: 5] [Impact Index Per Article: 2.5] [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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Gupta S, Dasmahapatra AK. Destabilization of Aβ fibrils by omega-3 polyunsaturated fatty acids: a molecular dynamics study. J Biomol Struct Dyn 2023; 41:581-598. [PMID: 34856889 DOI: 10.1080/07391102.2021.2009915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The senile plaques of neurotoxic aggregates of Aβ protein, deposited extraneuronally, mark the pathological hallmark of Alzheimer's disease (AD). The natural compounds such as omega-3 (ω-3) polyunsaturated fatty acids (PUFAs), which can access blood-brain barrier, are believed to be potential disruptors of preformed Aβ fibrils to cure AD with unknown mechanism. Herein, we present the destabilization potential of three ω-3 PUFAs, viz. Eicosapentaenoic acid (EPA), Docosahexaenoic acid (HXA), and α-linolenic acid (LNL) by molecular dynamics simulation. After an initial testing of 300 ns, EPA and HXA have been considered further for extended production run time, 500 ns. The increased value of root mean square deviation (RMSD), radius of gyration, and solvent-accessible surface area (SASA), the reduced number of H-bonds and β-sheet content, and disruption of salt bridges and hydrophobic contacts establish the binding of these ligands to Aβ fibril leading to destabilization. The polar head was found to interact with positively charged lysine (K28) residue in the fibril. However, the hydrophobicity of the long aliphatic tail competes with the intrinsic hydrophobic interactions of Aβ fibril. This amphiphilic nature of EPA and HXA led to the breaking of inherent hydrophobic contacts and formation of new bonds between the tail of PUFA and hydrophobic residues of Aβ fibril, leading to the destabilization of fibril. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) results explain the binding of EPA and HXA to Aβ fibril by interacting with different residues. The destabilization potential of EPA and HXA establishes them as promising drug leads to cure AD, and encourages prospecting of other fatty acids for therapeutic intervention in AD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shivani Gupta
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Ashok Kumar Dasmahapatra
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.,Center for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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7
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Boopathi S, Garduño‐Juárez R. Calcium inhibits penetration of Alzheimer's Aβ 1 - 42 monomers into the membrane. Proteins 2022; 90:2124-2143. [PMID: 36321654 PMCID: PMC9804374 DOI: 10.1002/prot.26403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/08/2022] [Accepted: 07/25/2022] [Indexed: 01/05/2023]
Abstract
Calcium ion regulation plays a crucial role in maintaining neuronal functions such as neurotransmitter release and synaptic plasticity. Copper (Cu2+ ) coordination to amyloid-β (Aβ) has accelerated Aβ1-42 aggregation that can trigger calcium dysregulation by enhancing the influx of calcium ions by extensive perturbing integrity of the membranes. Aβ1-42 aggregation, calcium dysregulation, and membrane damage are Alzheimer disease (AD) implications. To gain a detail of calcium ions' role in the full-length Aβ1-42 and Aβ1-42 -Cu2+ monomers contact, the cellular membrane before their aggregation to elucidate the neurotoxicity mechanism, we carried out 2.5 μs extensive molecular dynamics simulation (MD) to rigorous explorations of the intriguing feature of the Aβ1-42 and Aβ1-42 -Cu2+ interaction with the dimyristoylphosphatidylcholine (DMPC) bilayer in the presence of calcium ions. The outcome of the results compared to the same simulations without calcium ions. We surprisingly noted robust binding energies between the Aβ1-42 and membrane observed in simulations containing without calcium ions and is two and a half fold lesser in the simulation with calcium ions. Therefore, in the case of the absence of calcium ions, N-terminal residues of Aβ1-42 deeply penetrate from the surface to the center of the bilayer; in contrast to calcium ions presence, the N- and C-terminal residues are involved only in surface contacts through binding phosphate moieties. On the other hand, Aβ1-42 -Cu2+ actively participated in surface bilayer contacts in the absence of calcium ions. These contacts are prevented by forming a calcium bridge between Aβ1-42 -Cu2+ and the DMPC bilayer in the case of calcium ions presence. In a nutshell, Calcium ions do not allow Aβ1-42 penetration into the membranes nor contact of Aβ1-42 -Cu2+ with the membranes. These pieces of information imply that the calcium ions mediate the membrane perturbation via the monomer interactions but do not damage the membrane; they agree with the western blot experimental results of a higher concentration of calcium ions inhibit the membrane pore formation by Aβ peptides.
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Affiliation(s)
- Subramanian Boopathi
- Instituto de Ciencias FísicasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Ramón Garduño‐Juárez
- Instituto de Ciencias FísicasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
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8
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Roldán-Martín L, Peccati F, Sciortino G, Sodupe M, Maréchal JD. Impact of Cu(II) and Al(III) on the conformational landscape of amyloidβ 1-42. Phys Chem Chem Phys 2021; 23:13023-13032. [PMID: 34095932 DOI: 10.1039/d1cp01561c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Metal ions have been found to play an important role in the formation of extracellular β-amyloid plaques, a major hallmark of Alzheimer's disease. In the present study, the conformational landscape of Aβ42 with Al(iii) and Cu(ii) has been explored using Gaussian accelerated molecular dynamics. Both metals reduce the flexibility of the peptide and entail a higher structural organization, although to different degrees. As a general trend, Cu(ii) binding leads to an increased α-helix content and to the formation of two α-helices that tend to organize in a U-shape. By contrast, most Al(iii) complexes induce a decrease in helical content, leading to more extended structures that favor the appearance of transitory β-strands.
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Affiliation(s)
- Lorena Roldán-Martín
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - Francesca Peccati
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain. and Institut of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), 43007 Tarragona, Catalonia, Spain
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
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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: 462] [Impact Index Per Article: 115.5] [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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Lakey-Beitia J, Burillo AM, Penna GL, Hegde ML, Rao K. Polyphenols as Potential Metal Chelation Compounds Against Alzheimer's Disease. J Alzheimers Dis 2021; 82:S335-S357. [PMID: 32568200 PMCID: PMC7809605 DOI: 10.3233/jad-200185] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease affecting more than 50 million people worldwide. The pathology of this multifactorial disease is primarily characterized by the formation of amyloid-β (Aβ) aggregates; however, other etiological factors including metal dyshomeostasis, specifically copper (Cu), zinc (Zn), and iron (Fe), play critical role in disease progression. Because these transition metal ions are important for cellular function, their imbalance can cause oxidative stress that leads to cellular death and eventual cognitive decay. Importantly, these transition metal ions can interact with the amyloid-β protein precursor (AβPP) and Aβ42 peptide, affecting Aβ aggregation and increasing its neurotoxicity. Considering how metal dyshomeostasis may substantially contribute to AD, this review discusses polyphenols and the underlying chemical principles that may enable them to act as natural chelators. Furthermore, polyphenols have various therapeutic effects, including antioxidant activity, metal chelation, mitochondrial function, and anti-amyloidogenic activity. These combined therapeutic effects of polyphenols make them strong candidates for a moderate chelation-based therapy for AD.
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Affiliation(s)
- Johant Lakey-Beitia
- Centre for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, City of Knowledge, Panama
| | - Andrea M. Burillo
- Centre for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, City of Knowledge, Panama
| | - Giovanni La Penna
- National Research Council, Institute of Chemistry of Organometallic Compounds, Sesto Fiorentino (FI), Italy
| | - Muralidhar L. Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, USA
- Weill Medical College of Cornell University, New York, NY, USA
| | - K.S. Rao
- Centre for Neuroscience, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, City of Knowledge, Panama
- Zhongke Jianlan Medical Institute, Hangzhou, Republic of China
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11
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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: 7] [Impact Index Per Article: 1.4] [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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Huy Pham DQ, Krupa P, Nguyen HL, La Penna G, Li MS. Computational Model to Unravel the Function of Amyloid-β Peptides in Contact with a Phospholipid Membrane. J Phys Chem B 2020; 124:3300-3314. [DOI: 10.1021/acs.jpcb.0c00771] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Dinh Quoc Huy Pham
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Pawel Krupa
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Hoang Linh Nguyen
- Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward, Thu
Duc District, 00133 Ho Chi Minh City, Vietnam
| | - Giovanni La Penna
- National Research Council of Italy (CNR), Institute for Chemistry of Organometallic Compounds (ICCOM), 50019 Florence, Italy
- National Institute for Nuclear Physics (INFN), Section of Roma-Tor Vergata, 00186 Roma, Italy
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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13
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Gupta S, Dasmahapatra AK. Destabilization potential of phenolics on Aβ fibrils: mechanistic insights from molecular dynamics simulation. Phys Chem Chem Phys 2020; 22:19643-19658. [DOI: 10.1039/d0cp02459g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ellagic acid from pomegranate and walnuts is found to destabilize Aβ fibrils. It can be a potential drug to treat AD.
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Affiliation(s)
- Shivani Gupta
- Department of Chemical Engineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Ashok Kumar Dasmahapatra
- Department of Chemical Engineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
- Center for Nanotechnology
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14
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Effects of Cu(II) on the aggregation of amyloid-β. J Biol Inorg Chem 2019; 24:1197-1215. [PMID: 31602542 DOI: 10.1007/s00775-019-01727-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/01/2019] [Indexed: 12/27/2022]
Abstract
Aberrant aggregation of the Aβ protein is a hallmark of Alzheimer's disease (AD), but no complete characterization of the molecular level pathogenesis has been achieved. A promising hypothesis is that dysfunction of metal ion homeostasis, and consequently, the undesired interaction of metal ions with Aβ, may be central to the development of AD. Qualitatively, most data indicate that Cu(II) induces rapid self-assembly of both Aβ40 and Aβ42 during the initial phase of the aggregation, while at longer time scales fibrillation may occur, depending on the experimental conditions. For Aβ40 and Cu(II):Aβ ≤ 1, most data imply that low concentration of Aβ40 favors nucleation and rapid fibril elongation, while high concentration of Aβ40 favors formation of amorphous aggregates. However, there are conflicting reports on this issue. For Aβ42 and Cu(II):Aβ ≤ 1, there is consensus that the lag time is extended upon addition of Cu(II). For Cu(II):Aβ > 1, the lag time is increased upon interaction with Cu(II), and in most cases fibrillation is not observed, presumably because Cu(II) occupies a second more solvent-exposed binding site, which is more prone to form metal ion-bridged species and cause rapid formation of non-fibrillar aggregates. The interesting N-terminally truncated Aβ11-40 with high affinity for Cu(II), exhibits delay of fibrillation upon addition of 0.4 eq. Cu(II). In our view, there are still problems achieving reproducible results in this field, and we provide a shortlist of some of the pitfalls. Finally, we propose a consensus model for the effects of Cu(II) on the aggregation kinetics of Aβ.
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15
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Krupa P, Quoc Huy PD, Li MS. Properties of monomeric Aβ42 probed by different sampling methods and force fields: Role of energy components. J Chem Phys 2019. [DOI: 10.1063/1.5093184] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Pawel Krupa
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Pham Dinh Quoc Huy
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
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16
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Semenyuk P, Muronetz V. Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications. Int J Mol Sci 2019; 20:E1252. [PMID: 30871103 PMCID: PMC6429204 DOI: 10.3390/ijms20051252] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/18/2022] Open
Abstract
Interaction of proteins with charged macromolecules is involved in many processes in cells. Firstly, there are many naturally occurred charged polymers such as DNA and RNA, polyphosphates, sulfated glycosaminoglycans, etc., as well as pronouncedly charged proteins such as histones or actin. Electrostatic interactions are also important for "generic" proteins, which are not generally considered as polyanions or polycations. Finally, protein behavior can be altered due to post-translational modifications such as phosphorylation, sulfation, and glycation, which change a local charge of the protein region. Herein we review molecular modeling for the investigation of such interactions, from model polyanions and polycations to unfolded proteins. We will show that electrostatic interactions are ubiquitous, and molecular dynamics simulations provide an outstanding opportunity to look inside binding and reveal the contribution of electrostatic interactions. Since a molecular dynamics simulation is only a model, we will comprehensively consider its relationship with the experimental data.
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Affiliation(s)
- Pavel Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
| | - Vladimir Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia.
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La Penna G, Li MS. Computational models explain how copper binding to amyloid-β peptide oligomers enhances oxidative pathways. Phys Chem Chem Phys 2019; 21:8774-8784. [DOI: 10.1039/c9cp00293f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Amyloid-β (Aβ) peptides are intrinsically disordered peptides and their aggregation is the major hallmark of Alzheimer's disease (AD) development.
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Affiliation(s)
- Giovanni La Penna
- National Research Council of Italy (CNR)
- Institute for Chemistry of Organometallic Compounds (ICCOM)
- via Madonna del Piano 10
- 50019 Sesto Fiorentino
- Firenze
| | - Mai Suan Li
- Institute of Physics
- Polish Academy of Sciences
- Al. Lotnikow 32/46
- 02-668 Warsaw
- Poland
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