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Deng Y, Gao G, Yu L, Zhang Z, Zhang B, Li H, Zhang X, Shen L, Sun T. Engineering Core/Ligands Interfacial Anchors of Nanoparticles for Efficiently Inhibiting Both Aβ and Amylin Fibrillization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2312046. [PMID: 38829034 DOI: 10.1002/smll.202312046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/03/2024] [Indexed: 06/05/2024]
Abstract
Accurate construction of artificial nano-chaperones' structure is crucial for precise regulation of protein conformational transformation, facilitating effective treatment of proteopathy. However, how the ligand-anchors of nano-chaperones affect the spatial conformational changes in proteins remains unclear, limiting the development of efficient nano-chaperones. In this study, three types of gold nanoparticles (AuNPs) with different core/ligands interface anchor structures (Au─NH─R, Au─S─R, and Au─C≡C─R, R = benzoic acid) are synthesized as an ideal model to investigate the effect of interfacial anchors on Aβ and amylin fibrillization. Computational results revealed that the distinct interfacial anchors imparted diverse distributions of electrostatic potential on the nanointerface and core/ligands bond strength of AuNPs, leading to differential interactions with amyloid peptides. Experimental results demonstrated that all three types of AuNPs exhibit site-specific inhibitory effects on Aβ40 fibrillization due to preferential binding. For amylin, amino-anchored AuNPs demonstrate strong adsorption to multiple sites on amylin and effectively inhibit fibrillization. Conversely, thiol- and alkyne-anchored AuNPs adsorb at the head region of amylin, promoting folding and fibrillization. This study not only provided molecular insights into how core/ligands interfacial anchors of nanomaterials induce spatial conformational changes in amyloid peptides but also offered guidance for precisely engineering artificial-chaperones' nanointerfaces to regulate the conformational transformation of proteins.
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Affiliation(s)
- Yuzhou Deng
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Guanbin Gao
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
- Hubei Key Laboratory of Nanomedicine for Neurodegenerative Diseases, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Liangchong Yu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Zijun Zhang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Bin Zhang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Hu Li
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Xinyu Zhang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Lei Shen
- Hubei Key Laboratory of Nanomedicine for Neurodegenerative Diseases, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
- Hubei Key Laboratory of Nanomedicine for Neurodegenerative Diseases, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China
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Zhang M, Li Y, Han C, Chu S, Yu P, Cheng W. Biosynthesis of Nanoparticles with Green Tea for Inhibition of β-Amyloid Fibrillation Coupled with Ligands Analysis. Int J Nanomedicine 2024; 19:4299-4317. [PMID: 38766654 PMCID: PMC11102095 DOI: 10.2147/ijn.s451070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/17/2024] [Indexed: 05/22/2024] Open
Abstract
Background Inhibition of amyloid β protein fragment (Aβ) aggregation is considered to be one of the most effective strategies for the treatment of Alzheimer's disease. (-)-Epigallocatechin-3-gallate (EGCG) has been found to be effective in this regard; however, owing to its low bioavailability, nanodelivery is recommended for practical applications. Compared to chemical reduction methods, biosynthesis avoids possible biotoxicity and cumbersome preparation processes. Materials and Methods The interaction between EGCG and Aβ42 was simulated by molecular docking, and green tea-conjugated gold nanoparticles (GT-Au NPs) and EGCG-Au NPs were synthesized using EGCG-enriched green tea and EGCG solutions, respectively. Surface active molecules of the particles were identified and analyzed using various liquid chromatography-tandem triple quadrupole mass spectrometry methods. ThT fluorescence assay, circular dichroism, and TEM were used to investigate the effect of synthesized particles on the inhibition of Aβ42 aggregation. Results EGCG as well as apigenin, quercetin, baicalin, and glutathione were identified as capping ligands stabilized on the surface of GT-Au NPs. They more or less inhibited Aβ42 aggregation or promoted fibril disaggregation, with EGCG being the most effective, which bound to Aβ42 through hydrogen bonding, hydrophobic interactions, etc. resulting in 39.86% and 88.50% inhibition of aggregation and disaggregation effects, respectively. EGCG-Au NPs were not as effective as free EGCG, whereas multiple thiols and polyphenols in green tea accelerated and optimized heavy metal detoxification. The synthesized GT-Au NPs conferred the efficacy of diverse ligands to the particles, with inhibition of aggregation and disaggregation effects of 54.69% and 88.75%, respectively, while increasing the yield, enhancing water solubility, and decreasing cost. Conclusion Biosynthesis of nanoparticles using green tea is a promising simple and economical drug-carrying approach to confer multiple pharmacophore molecules to Au NPs. This could be used to design new drug candidates to treat Alzheimer's disease.
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Affiliation(s)
- Mai Zhang
- Mass Spectrometry Application Center, Tianjin Guoke Medical Technology Development Co., Ltd, Tianjin, People’s Republic of China
| | - Yan Li
- Mass Spectrometry Application Center, Tianjin Guoke Medical Technology Development Co., Ltd, Tianjin, People’s Republic of China
- Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences (CAS), Suzhou, People’s Republic of China
| | - Chunli Han
- Mass Spectrometry Application Center, Shandong CAS Intelligent Manufacturing Medical Device Technology Co., Ltd, Zaozhuang, People’s Republic of China
| | - Shiying Chu
- Mass Spectrometry Application Center, Tianjin Guoke Medical Technology Development Co., Ltd, Tianjin, People’s Republic of China
| | - Peng Yu
- Mass Spectrometry Application Center, Tianjin Guoke Medical Technology Development Co., Ltd, Tianjin, People’s Republic of China
| | - Wenbo Cheng
- Mass Spectrometry Application Center, Tianjin Guoke Medical Technology Development Co., Ltd, Tianjin, People’s Republic of China
- Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences (CAS), Suzhou, People’s Republic of China
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Eisenberg D, Hou K, Ge P, Sawaya M, Dolinsky J, Yang Y, Jiang YX, Lutter L, Boyer D, Cheng X, Pi J, Zhang J, Lu J, Yang S, Yu Z, Feigon J. How short peptides can disassemble ultra-stable tau fibrils extracted from Alzheimer's disease brain by a strain-relief mechanism. RESEARCH SQUARE 2024:rs.3.rs-4152095. [PMID: 38766197 PMCID: PMC11100904 DOI: 10.21203/rs.3.rs-4152095/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Reducing fibrous aggregates of protein tau is a possible strategy for halting progression of Alzheimer's dis-ease (AD). Previously we found that in vitro the D-peptide D-TLKIVWC disassembles tau fibrils from AD brains (AD-tau) into benign segments with no energy source present beyond ambient thermal agitation. This disassembly by a short peptide was unexpected, given that AD-tau is sufficiently stable to withstand disas-sembly in boiling SDS detergent. To consider D peptide-mediated disassembly as a potential therapeutic for AD, it is essential to understand the mechanism and energy source of the disassembly action. We find as-sembly of D-peptides into amyloid-like fibrils is essential for tau fibril disassembly. Cryo-EM and atomic force microscopy reveal that these D-peptide fibrils have a right-handed twist and embrace tau fibrils which have a left-handed twist. In binding to the AD-tau fibril, the oppositely twisted D-peptide fibril produces a strain, which is relieved by the disassembly of both fibrils. This strain-relief mechanism appears to operate in other examples of amyloid fibril disassembly and provides a new direction for the development of first-in-class therapeutics for amyloid diseases.
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Affiliation(s)
| | - Ke Hou
- University of California, Los Angeles
| | - Peng Ge
- University of California, Los Angeles
| | | | | | - Yuan Yang
- University of California Los Angeles
| | | | | | | | | | - Justin Pi
- University of California, Los Angeles
| | | | - Jiahui Lu
- University of California, Los Angeles
| | - Shixin Yang
- Janelia Research Campus, Howard Hughes Medical Institute
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Hou K, Pan H, Shahpasand-Kroner H, Hu C, Abskharon R, Seidler P, Mekkittikul M, Balbirnie M, Lantz C, Sawaya MR, Dolinsky JL, Jones M, Zuo X, Loo JA, Frautschy S, Cole G, Eisenberg DS. D-peptide-magnetic nanoparticles fragment tau fibrils and rescue behavioral deficits in a mouse model of Alzheimer's disease. SCIENCE ADVANCES 2024; 10:eadl2991. [PMID: 38691615 PMCID: PMC11062580 DOI: 10.1126/sciadv.adl2991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 03/29/2024] [Indexed: 05/03/2024]
Abstract
Amyloid fibrils of tau are increasingly accepted as a cause of neuronal death and brain atrophy in Alzheimer's disease (AD). Diminishing tau aggregation is a promising strategy in the search for efficacious AD therapeutics. Previously, our laboratory designed a six-residue, nonnatural amino acid inhibitor D-TLKIVW peptide (6-DP), which can prevent tau aggregation in vitro. However, it cannot block cell-to-cell transmission of tau aggregation. Here, we find D-TLKIVWC (7-DP), a d-cysteine extension of 6-DP, not only prevents tau aggregation but also fragments tau fibrils extracted from AD brains to neutralize their seeding ability and protect neuronal cells from tau-induced toxicity. To facilitate the transport of 7-DP across the blood-brain barrier, we conjugated it to magnetic nanoparticles (MNPs). The MNPs-DP complex retains the inhibition and fragmentation properties of 7-DP alone. Ten weeks of MNPs-DP treatment appear to reverse neurological deficits in the PS19 mouse model of AD. This work offers a direction for development of therapies to target tau fibrils.
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Affiliation(s)
- Ke Hou
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Hope Pan
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Hedieh Shahpasand-Kroner
- Department of Neurology, UCLA, Los Angeles, CA, USA
- Veterans Administration Greater Los Angeles Healthcare System, Geriatric Research and Clinical Core, Los Angeles, CA, USA
- Department of Medicine, UCLA, Los Angeles, CA, USA
| | - Carolyn Hu
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Romany Abskharon
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Paul Seidler
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Marisa Mekkittikul
- Department of Neurology, UCLA, Los Angeles, CA, USA
- Veterans Administration Greater Los Angeles Healthcare System, Geriatric Research and Clinical Core, Los Angeles, CA, USA
- Department of Medicine, UCLA, Los Angeles, CA, USA
| | - Melinda Balbirnie
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Carter Lantz
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
| | - Michael R. Sawaya
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Joshua L. Dolinsky
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
| | - Mychica Jones
- Department of Neurology, UCLA, Los Angeles, CA, USA
- Veterans Administration Greater Los Angeles Healthcare System, Geriatric Research and Clinical Core, Los Angeles, CA, USA
- Department of Medicine, UCLA, Los Angeles, CA, USA
| | - Xiaohong Zuo
- Department of Neurology, UCLA, Los Angeles, CA, USA
- Veterans Administration Greater Los Angeles Healthcare System, Geriatric Research and Clinical Core, Los Angeles, CA, USA
- Department of Medicine, UCLA, Los Angeles, CA, USA
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Sally Frautschy
- Department of Neurology, UCLA, Los Angeles, CA, USA
- Veterans Administration Greater Los Angeles Healthcare System, Geriatric Research and Clinical Core, Los Angeles, CA, USA
- Department of Medicine, UCLA, Los Angeles, CA, USA
| | - Greg Cole
- Department of Neurology, UCLA, Los Angeles, CA, USA
- Veterans Administration Greater Los Angeles Healthcare System, Geriatric Research and Clinical Core, Los Angeles, CA, USA
- Department of Medicine, UCLA, Los Angeles, CA, USA
| | - David S. Eisenberg
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Los Angeles, CA, USA
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5
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Duan P, El Mammeri N, Hong M. Milligram-scale assembly and NMR fingerprint of tau fibrils adopting the Alzheimer's disease fold. J Biol Chem 2024; 300:107326. [PMID: 38679331 PMCID: PMC11145547 DOI: 10.1016/j.jbc.2024.107326] [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: 02/28/2024] [Revised: 04/10/2024] [Accepted: 04/18/2024] [Indexed: 05/01/2024] Open
Abstract
In the Alzheimer's disease (AD) brain, the microtubule-associated protein tau aggregates into paired helical filaments in which each protofilament has a C-shaped conformation. In vitro assembly of tau fibrils adopting this fold is highly valuable for both fundamental and applied studies of AD without requiring patient-brain extracted fibrils. To date, reported methods for forming AD-fold tau fibrils have been irreproducible and sensitive to subtle variations in fibrillization conditions. Here, we describe a route to reproducibly assemble tau fibrils adopting the AD fold on the multi-milligram scale. We investigated the fibrillization conditions of two constructs and found that a tau (297-407) construct that contains four AD phospho-mimetic glutamate mutations robustly formed the C-shaped conformation. 2D and 3D correlation solid-state NMR spectra show a single predominant set of chemical shifts, indicating a single molecular conformation. Negative-stain electron microscopy and cryo-EM data confirm that the protofilament formed by 4E-tau (297-407) adopts the C-shaped conformation, which associates into paired, triple, and quadruple helical filaments. In comparison, NMR spectra indicate that a previously reported construct, tau (297-391), forms a mixture of a four-layered dimer structure and the C-shaped structure, whose populations are sensitive to the environmental conditions. The determination of the NMR chemical shifts of the AD-fold tau opens the possibility for future studies of tau fibril conformations and ligand binding by NMR. The quantitative assembly of tau fibrils adopting the AD fold should facilitate the development of diagnostic and therapeutic compounds that target AD tau.
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Affiliation(s)
- Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Nadia El Mammeri
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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6
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Balczon R, Lin MT, Voth S, Nelson AR, Schupp JC, Wagener BM, Pittet JF, Stevens T. Lung endothelium, tau, and amyloids in health and disease. Physiol Rev 2024; 104:533-587. [PMID: 37561137 DOI: 10.1152/physrev.00006.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/26/2023] [Accepted: 08/04/2023] [Indexed: 08/11/2023] Open
Abstract
Lung endothelia in the arteries, capillaries, and veins are heterogeneous in structure and function. Lung capillaries in particular represent a unique vascular niche, with a thin yet highly restrictive alveolar-capillary barrier that optimizes gas exchange. Capillary endothelium surveys the blood while simultaneously interpreting cues initiated within the alveolus and communicated via immediately adjacent type I and type II epithelial cells, fibroblasts, and pericytes. This cell-cell communication is necessary to coordinate the immune response to lower respiratory tract infection. Recent discoveries identify an important role for the microtubule-associated protein tau that is expressed in lung capillary endothelia in the host-pathogen interaction. This endothelial tau stabilizes microtubules necessary for barrier integrity, yet infection drives production of cytotoxic tau variants that are released into the airways and circulation, where they contribute to end-organ dysfunction. Similarly, beta-amyloid is produced during infection. Beta-amyloid has antimicrobial activity, but during infection it can acquire cytotoxic activity that is deleterious to the host. The production and function of these cytotoxic tau and amyloid variants are the subject of this review. Lung-derived cytotoxic tau and amyloid variants are a recently discovered mechanism of end-organ dysfunction, including neurocognitive dysfunction, during and in the aftermath of infection.
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Affiliation(s)
- Ron Balczon
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, United States
- Center for Lung Biology, University of South Alabama, Mobile, Alabama, United States
| | - Mike T Lin
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, Alabama, United States
- Center for Lung Biology, University of South Alabama, Mobile, Alabama, United States
| | - Sarah Voth
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine, Monroe, Louisiana, United States
| | - Amy R Nelson
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, Alabama, United States
- Center for Lung Biology, University of South Alabama, Mobile, Alabama, United States
| | - Jonas C Schupp
- Pulmonary and Critical Care Medicine, Department of Internal Medicine, Yale University, New Haven, Connecticut, United States
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
- German Center for Lung Research (DZL), Hannover, Germany
| | - Brant M Wagener
- Department of Anesthesiology and Perioperative Medicine, University of Alabama-Birmingham, Birmingham, Alabama, United States
| | - Jean-Francois Pittet
- Department of Anesthesiology and Perioperative Medicine, University of Alabama-Birmingham, Birmingham, Alabama, United States
| | - Troy Stevens
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, Alabama, United States
- Department of Internal Medicine, University of South Alabama, Mobile, Alabama, United States
- Center for Lung Biology, University of South Alabama, Mobile, Alabama, United States
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7
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Hou K, Ge P, Sawaya MR, Dolinsky JL, Yang Y, Jiang YX, Lutter L, Boyer DR, Cheng X, Pi J, Zhang J, Lu J, Yang S, Yu Z, Feigon J, Eisenberg DS. How short peptides can disassemble ultra-stable tau fibrils extracted from Alzheimer's disease brain by a strain-relief mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586668. [PMID: 38585812 PMCID: PMC10996594 DOI: 10.1101/2024.03.25.586668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Reducing fibrous aggregates of protein tau is a possible strategy for halting progression of Alzheimer's disease (AD). Previously we found that in vitro the D-peptide D-TLKIVWC disassembles tau fibrils from AD brains (AD-tau) into benign segments with no energy source present beyond ambient thermal agitation. This disassembly by a short peptide was unexpected, given that AD-tau is sufficiently stable to withstand disassembly in boiling SDS detergent. To consider D peptide-mediated disassembly as a potential therapeutic for AD, it is essential to understand the mechanism and energy source of the disassembly action. We find assembly of D-peptides into amyloid-like fibrils is essential for tau fibril disassembly. Cryo-EM and atomic force microscopy reveal that these D-peptide fibrils have a right-handed twist and embrace tau fibrils which have a left-handed twist. In binding to the AD-tau fibril, the oppositely twisted D-peptide fibril produces a strain, which is relieved by disassembly of both fibrils. This strain-relief mechanism appears to operate in other examples of amyloid fibril disassembly and provides a new direction for the development of first-in-class therapeutics for amyloid diseases.
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8
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Imtiaz A, Shimonaka S, Uddin MN, Elahi M, Ishiguro K, Hasegawa M, Hattori N, Motoi Y. Selection of lansoprazole from an FDA-approved drug library to inhibit the Alzheimer's disease seed-dependent formation of tau aggregates. Front Aging Neurosci 2024; 16:1368291. [PMID: 38633982 PMCID: PMC11022852 DOI: 10.3389/fnagi.2024.1368291] [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: 01/10/2024] [Accepted: 03/15/2024] [Indexed: 04/19/2024] Open
Abstract
The efficacy of current treatments is still insufficient for Alzheimer's disease (AD), the most common cause of Dementia. Out of the two pathological hallmarks of AD amyloid-β plaques and neurofibrillary tangles, comprising of tau protein, tau pathology strongly correlates with the symptoms of AD. Previously, screening for inhibitors of tau aggregation that target recombinant tau aggregates have been attempted. Since a recent cryo-EM analysis revealed distinct differences in the folding patterns of heparin-induced recombinant tau filaments and AD tau filaments, this study focused on AD seed-dependent tau aggregation in drug repositioning for AD. We screened 763 compounds from an FDA-approved drug library using an AD seed-induced tau aggregation in SH-SY5Y cell-based assay. In the first screening, 180 compounds were selected, 72 of which were excluded based on the results of lactate dehydrogenase assay. In the third screening with evaluations of soluble and insoluble tau, 38 compounds were selected. In the fourth screening with 3 different AD seeds, 4 compounds, lansoprazole, calcipotriene, desogestrel, and pentamidine isethionate, were selected. After AD seed-induced real-time quaking-induced conversion, lansoprazole was selected as the most suitable drug for repositioning. The intranasal administration of lansoprazole for 4 months to AD seed-injected mice improved locomotor activity and reduced both the amount of insoluble tau and the extent of phosphorylated tau-positive areas. Alanine replacement of the predicted binding site to an AD filament indicated the involvement of Q351, H362, and K369 in lansoprazole and C-shaped tau filaments. These results suggest the potential of lansoprazole as a candidate for drug repositioning to an inhibitor of tau aggregate formation in AD.
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Affiliation(s)
- Ahmed Imtiaz
- Department of Diagnosis, Prevention and Treatment of Dementia, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
- Department of Neurology, Juntendo University School of Medicine, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Shotaro Shimonaka
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Mohammad Nasir Uddin
- Department of Biochemistry & Molecular Biology, Faculty of Life Science, Mawlana Bhashani Science & Technology University, Tangail, Bangladesh
| | - Montasir Elahi
- Center for Birth Defect Research, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Koichi Ishiguro
- Department of Neurology, Juntendo University School of Medicine, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Masato Hasegawa
- Department of Brain and Neuroscience, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Yumiko Motoi
- Medical Center for Dementia, Juntendo University Hospital, Bunkyo-ku, Tokyo, Japan
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9
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Mammeri NE, Dregni AJ, Duan P, Hong M. Structures of AT8 and PHF1 phosphomimetic tau: Insights into the posttranslational modification code of tau aggregation. Proc Natl Acad Sci U S A 2024; 121:e2316175121. [PMID: 38408247 DOI: 10.1073/pnas.2316175121] [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: 09/17/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024] Open
Abstract
The microtubule-associated protein tau aggregates into amyloid fibrils in Alzheimer's disease and other neurodegenerative diseases. In these tauopathies, tau is hyperphosphorylated, suggesting that this posttranslational modification (PTM) may induce tau aggregation. Tau is also phosphorylated in normal developing brains. To investigate how tau phosphorylation induces amyloid fibrils, here we report the atomic structures of two phosphomimetic full-length tau fibrils assembled without anionic cofactors. We mutated key Ser and Thr residues to Glu in two regions of the protein. One construct contains three Glu mutations at the epitope of the anti-phospho-tau antibody AT8 (AT8-3E tau), whereas the other construct contains four Glu mutations at the epitope of the antibody PHF1 (PHF1-4E tau). Solid-state NMR data show that both phosphomimetic tau mutants form homogeneous fibrils with a single set of chemical shifts. The AT8-3E tau rigid core extends from the R3 repeat to the C terminus, whereas the PHF1-4E tau rigid core spans R2, R3, and R4 repeats. Cryoelectron microscopy data show that AT8-3E tau forms a triangular multi-layered core, whereas PHF1-4E tau forms a triple-stranded core. Interestingly, a construct combining all seven Glu mutations exhibits the same conformation as PHF1-4E tau. Scalar-coupled NMR data additionally reveal the dynamics and shape of the fuzzy coat surrounding the rigid cores. These results demonstrate that specific PTMs induce structurally specific tau aggregates, and the phosphorylation code of tau contains redundancy.
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Affiliation(s)
- Nadia El Mammeri
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Aurelio J Dregni
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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10
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Ahmad F, Karan A, Sharma R, Sharma NS, Sundar V, Jayaraj R, Mukherjee S, DeCoster MA. Evolving therapeutic interventions for the management and treatment of Alzheimer's disease. Ageing Res Rev 2024; 95:102229. [PMID: 38364913 DOI: 10.1016/j.arr.2024.102229] [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: 09/17/2023] [Revised: 12/11/2023] [Accepted: 02/10/2024] [Indexed: 02/18/2024]
Abstract
Alzheimer's Disease (AD) patients experience diverse symptoms, including memory loss, cognitive impairment, behavioral abnormalities, mood changes, and mental issues. The fundamental objective of this review is to discuss novel therapeutic approaches, with special emphasis on recently approved marketed formulations for the treatment of AD, especially Aducanumab, the first FDA approved moiety that surpasses the blood-brain barrier (BBB) and reduces amyloid plaques in the brain, thereby reducing associated cognitive decline. However, it is still in the phase IV trial and is to be completed by 2030. Other drugs such as lecanemab are also under clinical trial and has recently been approved by the FDA and is also discussed here. In this review, we also focus on active and passive immunotherapy for AD as well as several vaccines, such as amyloid-beta epitope-based vaccines, amyloid-beta DNA vaccines, and stem cell therapy for AD, which are in clinical trials. Furthermore, ongoing pre-clinical trials associated with AD and other novel strategies such as curcumin-loaded nanoparticles, Crispr/ cas9, precision medicine, as well as some emerging therapies like anti-sense therapy are also highlighted. Additionally, we discuss some off-labeled drugs like non-steroidal anti-inflammatory drugs (NSAID), anti-diabetic drugs, and lithium, which can manage symptoms of AD and different non-pharmacological approaches are also covered which can help to manage AD. In summary, we have tried to cover all the therapeutic interventions which are available for the treatment and management of AD under sections approved, clinical phase, pre-clinical phase or futuristic interventions, off-labelled drugs, and non-pharmacological interventions for AD, offering positive findings and well as challenges that remain.
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Affiliation(s)
- Faizan Ahmad
- Department of Medical Elementology and Toxicology, Jamia Hamdard University, Delhi, India
| | - Anik Karan
- Department of Mechanical and Bioengineering, University of Kansas, Lawrence, KS, USA.
| | - Rashi Sharma
- Department of Biotechnology, Delhi Technological University, Bawana, Delhi, India
| | - Navatha Shree Sharma
- Department of Surgery Transplant, University of Nebraska Medical Centre, Omaha, NE, USA
| | - Vaishnavi Sundar
- Department of Internal Medicine, University of Nebraska Medical Centre, Omaha, NE, USA
| | - Richard Jayaraj
- Department of Paediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, UAE
| | - Sudip Mukherjee
- Biomedical Engineering, Indian Institute of Technology- Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Mark A DeCoster
- Cellular Neuroscience Laboratory, Biomedical Engineering, College of Engineering and Science, Louisiana Tech University, Ruston, LA, USA; Cellular Neuroscience Laboratory, Institute for Micromanufacturing, College of Engineering and Science, Louisiana Tech University, Ruston, LA, USA.
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11
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Duangjan C, Chang X, Seidler PM, Curran SP. Oolonghomobisflavans from Camellia sinensis disaggregate tau fibrils across Alzheimer's disease models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582120. [PMID: 38464186 PMCID: PMC10925199 DOI: 10.1101/2024.02.26.582120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Alzheimer's disease (AD) is a common debilitating neurodegenerative disease with limited treatment options. Amyloid-β (Aβ) and tau fibrils are well-established hallmarks of AD, which can induce oxidative stress, neuronal cell death, and are linked to disease pathology. Here, we describe the effects of Oolonghomobisflavan A (OFA) and Oolonghomobisflavan B (OFB) on tau fibril disaggregation and prionogenic seeding. Transcriptomic analysis of OF-treated animals reveals the induction of a proteostasis-enhancing and health-promoting signature. OFA treatment reduced the burden of Tau protein aggregation in a C. elegans model expressing pathogenic human tau ("hTau-expressing") and promoted Tau disaggregation and inhibited seeding in assays using ex vivo brain-derived paired helical filament tau protein fibrils from Alzheimer's disease brain donors. Correspondingly, treatment with OF improved multiple fitness and aging-related health parameters in the hTau-expressing C. elegans model, including reproductive output, muscle function, and importantly, reversed the shortened lifespan stemming from pathogenic Tau expression. Collectively, this study provides new evidence supporting the neuroprotective effects of OFs and reveal a new therapeutic strategy for targeting AD and other neurodegenerative diseases characterized by tauopathy.
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12
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Guarnieri L, Bosco F, Leo A, Citraro R, Palma E, De Sarro G, Mollace V. Impact of micronutrients and nutraceuticals on cognitive function and performance in Alzheimer's disease. Ageing Res Rev 2024; 95:102210. [PMID: 38296163 DOI: 10.1016/j.arr.2024.102210] [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: 07/31/2023] [Revised: 01/10/2024] [Accepted: 01/25/2024] [Indexed: 02/13/2024]
Abstract
Alzheimer's disease (AD) is a major global health problem today and is the most common form of dementia. AD is characterized by the formation of β-amyloid (Aβ) plaques and neurofibrillary clusters, leading to decreased brain acetylcholine levels in the brain. Another mechanism underlying the pathogenesis of AD is the abnormal phosphorylation of tau protein that accumulates at the level of neurofibrillary aggregates, and the areas most affected by this pathological process are usually the cholinergic neurons in cortical, subcortical, and hippocampal areas. These effects result in decreased cognitive function, brain atrophy, and neuronal death. Malnutrition and weight loss are the most frequent manifestations of AD, and these are also associated with greater cognitive decline. Several studies have confirmed that a balanced low-calorie diet and proper nutritional intake may be considered important factors in counteracting or slowing the progression of AD, whereas a high-fat or hypercholesterolemic diet predisposes to an increased risk of developing AD. Especially, fruits, vegetables, antioxidants, vitamins, polyunsaturated fatty acids, and micronutrients supplementation exert positive effects on aging-related changes in the brain due to their antioxidant, anti-inflammatory, and radical scavenging properties. The purpose of this review is to summarize some possible nutritional factors that may contribute to the progression or prevention of AD, understand the role that nutrition plays in the formation of Aβ plaques typical of this neurodegenerative disease, to identify some potential therapeutic strategies that may involve some natural compounds, in delaying the progression of the disease.
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Affiliation(s)
- Lorenza Guarnieri
- Section of Pharmacology, Science of Health Department, School of Medicine, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy
| | - Francesca Bosco
- Section of Pharmacology, Science of Health Department, School of Medicine, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy.
| | - Antonio Leo
- Section of Pharmacology, Science of Health Department, School of Medicine, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy; Research Center FAS@UMG, Department of Health Science, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy
| | - Rita Citraro
- Section of Pharmacology, Science of Health Department, School of Medicine, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy; Research Center FAS@UMG, Department of Health Science, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy
| | - Ernesto Palma
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Giovambattista De Sarro
- Section of Pharmacology, Science of Health Department, School of Medicine, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy; Research Center FAS@UMG, Department of Health Science, University "Magna Graecia" of Catanzaro, 88100 Catanzaro, Italy
| | - Vincenzo Mollace
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
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13
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Lama D, Vosselman T, Sahin C, Liaño-Pons J, Cerrato CP, Nilsson L, Teilum K, Lane DP, Landreh M, Arsenian Henriksson M. A druggable conformational switch in the c-MYC transactivation domain. Nat Commun 2024; 15:1865. [PMID: 38424045 PMCID: PMC10904854 DOI: 10.1038/s41467-024-45826-7] [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: 01/12/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
The c-MYC oncogene is activated in over 70% of all human cancers. The intrinsic disorder of the c-MYC transcription factor facilitates molecular interactions that regulate numerous biological pathways, but severely limits efforts to target its function for cancer therapy. Here, we use a reductionist strategy to characterize the dynamic and structural heterogeneity of the c-MYC protein. Using probe-based Molecular Dynamics (MD) simulations and machine learning, we identify a conformational switch in the c-MYC amino-terminal transactivation domain (termed coreMYC) that cycles between a closed, inactive, and an open, active conformation. Using the polyphenol epigallocatechin gallate (EGCG) to modulate the conformational landscape of coreMYC, we show through biophysical and cellular assays that the induction of a closed conformation impedes its interactions with the transformation/transcription domain-associated protein (TRRAP) and the TATA-box binding protein (TBP) which are essential for the transcriptional and oncogenic activities of c-MYC. Together, these findings provide insights into structure-activity relationships of c-MYC, which open avenues towards the development of shape-shifting compounds to target c-MYC as well as other disordered transcription factors for cancer treatment.
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Affiliation(s)
- Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden.
| | - Thibault Vosselman
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
- Department of Biology, Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Judit Liaño-Pons
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
| | - Carmine P Cerrato
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14813, Huddinge, Sweden
| | - Kaare Teilum
- Department of Biology, Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden.
- Department of Cell- and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.
| | - Marie Arsenian Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden.
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, SE-221 00, Lund, Sweden.
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14
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Bridges LR. RNA as a component of scrapie fibrils. Sci Rep 2024; 14:5011. [PMID: 38424114 PMCID: PMC10904389 DOI: 10.1038/s41598-024-55278-0] [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: 11/02/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
Recently, electron cryo-microscopy (cryo-EM) maps of fibrils from the brains of mice and hamsters with five infectious scrapie strains have been published and deposited in the electron microscopy data bank (EMDB). As noted by the primary authors, the fibrils contain a second component other than protein. The aim of the present study was to identify the nature of this second component in the published maps using an in silico approach. Extra densities (EDs) containing this component were continuous, straight, axial, at right angles to protein rungs and within hydrogen-bonding distance of protein, consistent with a structural role. EDs co-located with strips of basic residues, notably lysines, and formed a conspicuous cladding over parts of the N-terminal lobe of the protein. A Y-shaped polymer consistent with RNA was found, in places forming a single chain and at one location forming a duplex, comprising two antiparallel chains, and raising the intriguing possibility of replicative behaviour. To reflect the monotonous nature of the protein interface, it is suggested that the RNA may be a short tandem repeat. Fibrils from brains of patients with Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and other neurodegenerations also contain EDs and may be of a similar aetiology.
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Affiliation(s)
- Leslie R Bridges
- Neuropathology, Cellular Pathology, South West London Pathology, St George's Hospital, St George's University Hospitals NHS Foundation Trust, London, UK.
- Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK.
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15
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Bai H, Wu Y, Li H, Zhu Y, Che R, Wang F, Zhang C. Cerebral neurotoxicity of amino-modified polystyrene nanoplastics in mice and the protective effects of functional food Camellia pollen. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169511. [PMID: 38145676 DOI: 10.1016/j.scitotenv.2023.169511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/16/2023] [Accepted: 12/17/2023] [Indexed: 12/27/2023]
Abstract
Accumulating evidence suggests that nanoplastics contribute to an increased risk of brain damage, however, the precise underlying mechanisms remain unclear. Here, we subjected mice to long-term exposure to amino-modified polystyrene nanoplastics (APS-NPs). These nanoplastics were detected in the mouse brain; coupled with the observed upregulation of Alzheimer's disease-associated genes (APP and MAPT). To further explore nanoplastic damage mechanisms and the corresponding protective strategies against these mechanisms in vitro, we used hCMEC/D3 and HT22 cells. Results showed that APS-NPs disrupted tight junction proteins (Occludin and ZO-1) via TLR2/MMP9 axis, resulting in blood-brain barrier permeation; this was significantly mitigated by functional food Camellia pollen treatment. APS-NPs initiated iNOS and nNOS upregulation within neurons resulting in Sirtuin 1 deacetylase inactivation and CBP acetyltransferase stimulation, ultimately leading to Ac-Tau formation. This process was attenuated by Camellia pollen, which also ameliorated the APS-NPs-induced neuronal apoptosis mediated by the p53/Bax/Bcl-2 axis. Network pharmacology analysis of Camellia pollen offered a further theoretical understanding of its potential applications in preventing and treating nervous system disorders, such as Alzheimer's disease. This study established that Camellia pollen protects the brain against APS-NPs-mediated blood-brain barrier damage and alleviates neuronal apoptosis and Alzheimer's disease-like neurotoxicity. This study elucidates the mechanisms underlying polystyrene-induced brain damage and can be used to inform future prevention and treatment strategies.
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Affiliation(s)
- Hangjia Bai
- Sino-Jan Joint Lab of Natural Health Products Research, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Yanliang Wu
- Sino-Jan Joint Lab of Natural Health Products Research, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Haini Li
- Sino-Jan Joint Lab of Natural Health Products Research, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Yining Zhu
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 21094, China
| | - Ruijie Che
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 21094, China
| | - Fenghe Wang
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 21094, China.
| | - Chaofeng Zhang
- Sino-Jan Joint Lab of Natural Health Products Research, School of Traditional Chinese Medicines, China Pharmaceutical University, Nanjing 210009, China.
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16
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Rinauro DJ, Chiti F, Vendruscolo M, Limbocker R. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases. Mol Neurodegener 2024; 19:20. [PMID: 38378578 PMCID: PMC10877934 DOI: 10.1186/s13024-023-00651-2] [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: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 02/22/2024] Open
Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
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Affiliation(s)
- Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA.
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17
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Chisholm TS, Hunter CA. A closer look at amyloid ligands, and what they tell us about protein aggregates. Chem Soc Rev 2024; 53:1354-1374. [PMID: 38116736 DOI: 10.1039/d3cs00518f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The accumulation of amyloid fibrils is characteristic of neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease. Detecting these fibrils with fluorescent or radiolabelled ligands is one strategy for diagnosing and better understanding these diseases. A vast number of amyloid-binding ligands have been reported in the literature as a result. To obtain a better understanding of how amyloid ligands bind, we have compiled a database of 3457 experimental dissociation constants for 2076 unique amyloid-binding ligands. These ligands target Aβ, tau, or αSyn fibrils, as well as relevant biological samples including AD brain homogenates. From this database significant variation in the reported dissociation constants of ligands was found, possibly due to differences in the morphology of the fibrils being studied. Ligands were also found to bind to Aβ(1-40) and Aβ(1-42) fibrils with similar affinities, whereas a greater difference was found for binding to Aβ and tau or αSyn fibrils. Next, the binding of ligands to fibrils was shown to be largely limited by the hydrophobic effect. Some Aβ ligands do not fit into this hydrophobicity-limited model, suggesting that polar interactions can play an important role when binding to this target. Finally several binding site models were outlined for amyloid fibrils that describe what ligands target what binding sites. These models provide a foundation for interpreting and designing site-specific binding assays.
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Affiliation(s)
- Timothy S Chisholm
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1 EW, UK.
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1 EW, UK.
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18
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Bisi N, Pinzi L, Rastelli G, Tonali N. Early Diagnosis of Neurodegenerative Diseases: What Has Been Undertaken to Promote the Transition from PET to Fluorescence Tracers. Molecules 2024; 29:722. [PMID: 38338465 PMCID: PMC10856728 DOI: 10.3390/molecules29030722] [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: 01/04/2024] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Alzheimer's Disease (AD) and Parkinson's Disease (PD) represent two among the most frequent neurodegenerative diseases worldwide. A common hallmark of these pathologies is the misfolding and consequent aggregation of amyloid proteins into soluble oligomers and insoluble β-sheet-rich fibrils, which ultimately lead to neurotoxicity and cell death. After a hundred years of research on the subject, this is the only reliable histopathological feature in our hands. Since AD and PD are diagnosed only once neuronal death and the first symptoms have appeared, the early detection of these diseases is currently impossible. At present, there is no effective drug available, and patients are left with symptomatic and inconclusive therapies. Several reasons could be associated with the lack of effective therapeutic treatments. One of the most important factors is the lack of selective probes capable of detecting, as early as possible, the most toxic amyloid species involved in the onset of these pathologies. In this regard, chemical probes able to detect and distinguish among different amyloid aggregates are urgently needed. In this article, we will review and put into perspective results from ex vivo and in vivo studies performed on compounds specifically interacting with such early species. Following a general overview on the three different amyloid proteins leading to insoluble β-sheet-rich amyloid deposits (amyloid β1-42 peptide, Tau, and α-synuclein), a list of the advantages and disadvantages of the approaches employed to date is discussed, with particular attention paid to the translation of fluorescence imaging into clinical applications. Furthermore, we also discuss how the progress achieved in detecting the amyloids of one neurodegenerative disease could be leveraged for research into another amyloidosis. As evidenced by a critical analysis of the state of the art, substantial work still needs to be conducted. Indeed, the early diagnosis of neurodegenerative diseases is a priority, and we believe that this review could be a useful tool for better investigating this field.
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Affiliation(s)
- Nicolò Bisi
- Université Paris-Saclay, CNRS, BioCIS, Bat. Henri Moissan, 17, Av. des Sciences, 91400 Orsay, France
| | - Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy; (L.P.); (G.R.)
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy; (L.P.); (G.R.)
| | - Nicolò Tonali
- Université Paris-Saclay, CNRS, BioCIS, Bat. Henri Moissan, 17, Av. des Sciences, 91400 Orsay, France
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19
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Chen Z, Shan G, Wang X, Zuo Y, Song X, Ma Y, Zhao X, Jin Y. Top 100 most-cited articles on tau protein: a bibliometric analysis and evidence mapping. Front Neurosci 2024; 18:1345225. [PMID: 38356652 PMCID: PMC10864446 DOI: 10.3389/fnins.2024.1345225] [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: 11/27/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024] Open
Abstract
Background Tau, a microtubule-associated protein extensively distributed within the central nervous system (CNS), exhibits close associations with various neurodegenerative disorders. Here, we aimed to conduct a qualitative and quantitative bibliometric study of the top 100 most-cited publications on tau protein and reveal the current research hotspots and future perspectives. Methods The relevant literature was retrieved from the Web of Science Core Collection. CiteSpace (v6.2.R4) and VOSviewer (1.6.19) were adopted for bibliometric analysis with statistical and visual analysis. Results Citations per article ranged from 615 to 3,123, with a median number of 765.5 times. "Neuroscience" emerged as the most extensively researched subject in this field. The USA has emerged as the leading country, with a publication record (n = 65), total citations (n = 66,543), strong centrality (0.29), and extensive international collaborations. Harvard University (n = 11) and the University of California, San Francisco (n = 11) were the top two institutions in terms of publications. Neuron dominated with 13 articles in the 37 high-quality journals. M. Goedert from the MRC Laboratory of Molecular Biology was the most productive (n = 9) and top co-cited (n = 179) author. The most frequently studied keywords were Alzheimer's disease (n = 38). Future research is anticipated to intensify its focus on the pathogenesis of various tau-related diseases, emphasizing the phosphorylation and structural alterations of tau protein, particularly in Alzheimer's disease. Conclusion The pathogenesis of various tau-related diseases, including the phosphorylation and structural alterations of the tau protein, will be the primary focus of future research, with particular emphasis on Alzheimer's disease as a central area of investigation.
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Affiliation(s)
| | | | | | | | | | | | - Xin Zhao
- Department of Anesthesiology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yanwu Jin
- Department of Anesthesiology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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20
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Smith M, Knight IS, Kormos RC, Pepe JG, Kunach P, Diamond MI, Shahmoradian SH, Irwin JJ, DeGrado WF, Shoichet BK. Docking for Molecules That Bind in a Symmetric Stack with SymDOCK. J Chem Inf Model 2024; 64:425-434. [PMID: 38191997 PMCID: PMC10806807 DOI: 10.1021/acs.jcim.3c01749] [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: 10/29/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/10/2024]
Abstract
Discovering ligands for amyloid fibrils, such as those formed by the tau protein, is an area of great current interest. In recent structures, ligands bind in stacks in the tau fibrils to reflect the rotational and translational symmetry of the fibril itself; in these structures, the ligands make few interactions with the protein but interact extensively with each other. To exploit this symmetry and stacking, we developed SymDOCK, a method to dock molecules that follow the protein's symmetry. For each prospective ligand pose, we apply the symmetry operation of the fibril to generate a self-interacting and fibril-interacting stack, checking that doing so will not cause a clash between the original molecule and its image. Absent a clash, we retain that pose and add the ligand-ligand van der Waals energy to the ligand's docking score (here using DOCK3.8). We can check these geometries and energies using an implementation of ANI, a neural-network-based quantum-mechanical evaluation of the ligand stacking energies. In retrospective calculations, symmetry docking can reproduce the poses of three tau PET tracers whose structures have been determined. More convincingly, in a prospective study, SymDOCK predicted the structure of the PET tracer MK-6240 bound in a symmetrical stack to AD PHF tau before that structure was determined; the docked pose was used to determine how MK-6240 fit the cryo-EM density. In proof-of-concept studies, SymDOCK enriched known ligands over property-matched decoys in retrospective screens without sacrificing docking speed and can address large library screens that seek new symmetrical stackers. Future applications of this approach will be considered.
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Affiliation(s)
- Matthew
S. Smith
- Department
of Pharmaceutical Chemistry, University
of California, UCSF Genentech
Hall Box 2280, 600 16th St Rm 518,San Francisco, California 94158, United States
- Program
in Biophysics, University of California, UCSF Genentech Hall MC2240, 600
16th St Rm N474D,San Francisco, California 94143, United States
| | - Ian S. Knight
- Department
of Pharmaceutical Chemistry, University
of California, UCSF Genentech
Hall Box 2280, 600 16th St Rm 518,San Francisco, California 94158, United States
| | - Rian C. Kormos
- Department
of Pharmaceutical Chemistry, University
of California, UCSF Genentech
Hall Box 2280, 600 16th St Rm 518,San Francisco, California 94158, United States
- Program
in Biophysics, University of California, UCSF Genentech Hall MC2240, 600
16th St Rm N474D,San Francisco, California 94143, United States
| | - Joseph G. Pepe
- Department
of Pharmaceutical Chemistry, University
of California, UCSF Genentech
Hall Box 2280, 600 16th St Rm 518,San Francisco, California 94158, United States
- Program
in Biophysics, University of California, UCSF Genentech Hall MC2240, 600
16th St Rm N474D,San Francisco, California 94143, United States
| | - Peter Kunach
- McGill
Research Centre for Studies in Aging, McGill
University, 6875 Boulevard LaSalle, Montreal, Quebec H4H 1R3, Canada
- Department
of Neurology and Neurosurgery, McGill University, 1033 Pine Avenue West, Room 310, Montreal, Quebec H3A 1A1, Canada
- Center
for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell
Jr. Brain Institute, University of Texas
Southwestern Medical Center, 6124 Harry Hines Blvd. Suite NS03.200, Dallas, Texas 75390, United States
- Department
of Neurology, University of Texas Southwestern
Medical Center, 5323 Harry Hines Blvd., G2.222, Dallas, Texas 75390-9368, United States
- Department
of Neuroscience, University of Texas Southwestern
Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-9111, United States
| | - Marc I. Diamond
- Center
for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell
Jr. Brain Institute, University of Texas
Southwestern Medical Center, 6124 Harry Hines Blvd. Suite NS03.200, Dallas, Texas 75390, United States
- Department
of Neurology, University of Texas Southwestern
Medical Center, 5323 Harry Hines Blvd., G2.222, Dallas, Texas 75390-9368, United States
- Department
of Neuroscience, University of Texas Southwestern
Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-9111, United States
| | - Sarah H. Shahmoradian
- Center
for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell
Jr. Brain Institute, University of Texas
Southwestern Medical Center, 6124 Harry Hines Blvd. Suite NS03.200, Dallas, Texas 75390, United States
- Department
of Biophysics, University of Texas Southwestern
Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-8816, United States
| | - John J. Irwin
- Department
of Pharmaceutical Chemistry, University
of California, UCSF Genentech
Hall Box 2280, 600 16th St Rm 518,San Francisco, California 94158, United States
| | - William F. DeGrado
- Department
of Pharmaceutical Chemistry, University
of California, UCSF Genentech
Hall Box 2280, 600 16th St Rm 518,San Francisco, California 94158, United States
- Cardiovascular
Research Institute, University of California, 555 Mission Bay Blvd South, PO Box 589001, San Francisco, California 94158-9001, United
States
| | - Brian K. Shoichet
- Department
of Pharmaceutical Chemistry, University
of California, UCSF Genentech
Hall Box 2280, 600 16th St Rm 518,San Francisco, California 94158, United States
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21
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Tetter S, Arseni D, Murzin AG, Buhidma Y, Peak-Chew SY, Garringer HJ, Newell KL, Vidal R, Apostolova LG, Lashley T, Ghetti B, Ryskeldi-Falcon B. TAF15 amyloid filaments in frontotemporal lobar degeneration. Nature 2024; 625:345-351. [PMID: 38057661 PMCID: PMC10781619 DOI: 10.1038/s41586-023-06801-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/30/2023] [Indexed: 12/08/2023]
Abstract
Frontotemporal lobar degeneration (FTLD) causes frontotemporal dementia (FTD), the most common form of dementia after Alzheimer's disease, and is often also associated with motor disorders1. The pathological hallmarks of FTLD are neuronal inclusions of specific, abnormally assembled proteins2. In the majority of cases the inclusions contain amyloid filament assemblies of TAR DNA-binding protein 43 (TDP-43) or tau, with distinct filament structures characterizing different FTLD subtypes3,4. The presence of amyloid filaments and their identities and structures in the remaining approximately 10% of FTLD cases are unknown but are widely believed to be composed of the protein fused in sarcoma (FUS, also known as translocated in liposarcoma). As such, these cases are commonly referred to as FTLD-FUS. Here we used cryogenic electron microscopy (cryo-EM) to determine the structures of amyloid filaments extracted from the prefrontal and temporal cortices of four individuals with FTLD-FUS. Surprisingly, we found abundant amyloid filaments of the FUS homologue TATA-binding protein-associated factor 15 (TAF15, also known as TATA-binding protein-associated factor 2N) rather than of FUS itself. The filament fold is formed from residues 7-99 in the low-complexity domain (LCD) of TAF15 and was identical between individuals. Furthermore, we found TAF15 filaments with the same fold in the motor cortex and brainstem of two of the individuals, both showing upper and lower motor neuron pathology. The formation of TAF15 amyloid filaments with a characteristic fold in FTLD establishes TAF15 proteinopathy in neurodegenerative disease. The structure of TAF15 amyloid filaments provides a basis for the development of model systems of neurodegenerative disease, as well as for the design of diagnostic and therapeutic tools targeting TAF15 proteinopathy.
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Affiliation(s)
| | - Diana Arseni
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Yazead Buhidma
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, London, UK
| | | | - Holly J Garringer
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kathy L Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ruben Vidal
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Liana G Apostolova
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tammaryn Lashley
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, London, UK
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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22
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Abukhaled Y, Hatab K, Awadhalla M, Hamdan H. Understanding the genetic mechanisms and cognitive impairments in Down syndrome: towards a holistic approach. J Neurol 2024; 271:87-104. [PMID: 37561187 PMCID: PMC10769995 DOI: 10.1007/s00415-023-11890-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 08/11/2023]
Abstract
The most common genetic cause of intellectual disability is Down syndrome (DS), trisomy 21. It commonly results from three copies of human chromosome 21 (HC21). There are no mutations or deletions involved in DS. Instead, the phenotype is caused by altered transcription of the genes on HC21. These transcriptional variations are responsible for a myriad of symptoms affecting every organ system. A very debilitating aspect of DS is intellectual disability (ID). Although tremendous advances have been made to try and understand the underlying mechanisms of ID, there is a lack of a unified, holistic view to defining the cause and managing the cognitive impairments. In this literature review, we discuss the mechanisms of neuronal over-inhibition, abnormal morphology, and other genetic factors in contributing to the development of ID in DS patients and to gain a holistic understanding of ID in DS patients. We also highlight potential therapeutic approaches to improve the quality of life of DS patients.
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Affiliation(s)
- Yara Abukhaled
- Department of Physiology and Immunology, College of Medicine, and Health Sciences, Khalifa University, 127788, Abu Dhabi, United Arab Emirates
| | - Kenana Hatab
- Department of Physiology and Immunology, College of Medicine, and Health Sciences, Khalifa University, 127788, Abu Dhabi, United Arab Emirates
| | - Mohammad Awadhalla
- Department of Physiology and Immunology, College of Medicine, and Health Sciences, Khalifa University, 127788, Abu Dhabi, United Arab Emirates
| | - Hamdan Hamdan
- Department of Physiology and Immunology, College of Medicine, and Health Sciences, Khalifa University, 127788, Abu Dhabi, United Arab Emirates.
- Healthcare Engineering Innovation Center (HEIC), Khalifa University, 127788, Abu Dhabi, United Arab Emirates.
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23
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Nayak V, Patra S, Rout S, Jena AB, Sharma R, Pattanaik KP, Singh J, Pandey SS, Singh RP, Majhi S, Singh KR, Kerry RG. Regulation of neuroinflammation in Alzheimer's disease via nanoparticle-loaded phytocompounds with anti-inflammatory and autophagy-inducing properties. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 122:155150. [PMID: 37944239 DOI: 10.1016/j.phymed.2023.155150] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/23/2023] [Accepted: 10/14/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is characterized by neuroinflammation linked to amyloid β (Aβ) aggregation and phosphorylated tau (τ) protein in neurofibrillary tangles (NFTs). Key elements in Aβ production and NFT assembly, like γ-secretase and p38 mitogen-activated protein kinase (p38MAPK), contribute to neuroinflammation. In addition, impaired proteosomal and autophagic pathways increase Aβ and τ aggregation, leading to neuronal damage. Conventional neuroinflammation drugs have limitations due to unidirectional therapeutic approaches and challenges in crossing the Blood-Brain Barrier (BBB). Clinical trials for non-steroidal anti-inflammatory drugs (NSAIDs) and other therapeutics remain uncertain. Novel strategies addressing the complex pathogenesis and BBB translocation are needed to effectively tackle AD-related neuroinflammation. PURPOSE The current scenario demands for a much-sophisticated theranostic measures which could be achieved via customized engineering and designing of novel nanotherapeutics. As, these therapeutics functions as a double edge sword, having the efficiency of unambiguous targeting, multiple drug delivery and ability to cross BBB proficiently. METHODS Inclusion criteria involve selecting recent, English-language studies from the past decade (2013-2023) that explore the regulation of neuroinflammation in neuroinflammation, Alzheimer's disease, amyloid β, tau protein, nanoparticles, autophagy, and phytocompounds. Various study types, including clinical trials, experiments, and reviews, were considered. Exclusion criteria comprised non-relevant publication types, studies unrelated to Alzheimer's disease or phytocompounds, those with methodological flaws, duplicates, and studies with inaccessible data. RESULTS In this study, polymeric nanoparticles loaded with specific phytocompounds and coated with an antibody targeting the transferrin receptor (anti-TfR) present on BBB. Thereafter, the engineered nanoparticles with the ability to efficiently traverse the BBB and interact with target molecules within the brain, could induce autophagy, a cellular process crucial for neuronal health, and exhibit potent anti-inflammatory effects. Henceforth, the proposed combination of desired phytocompounds, polymeric nanoparticles, and anti-TfR coating presents a promising approach for targeted drug delivery to the brain, with potential implications in neuroinflammatory conditions such as Alzheimer's disease.
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Affiliation(s)
- Vinayak Nayak
- ICAR- National Institute on Foot and Mouth Disease-International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar, Odisha (752050), India
| | - Sushmita Patra
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra (410210), India
| | - Shrushti Rout
- Department of Biotechnology, Utkal University, Vani Vihar, Bhubaneswar, Odisha (751004), India
| | - Atala Bihari Jena
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (02115), United States of America
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh (221005), India
| | - Kali Prasad Pattanaik
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar 751024, India
| | - Jay Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh (221005), India
| | - Shyam S Pandey
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu, Kitakyushu (8080196), Japan
| | - Ravindra Pratap Singh
- Department of Biotechnology, Faculty of Science, Indira Gandhi National Tribal University, Amarkantak, Madhya Pradesh 484887, India
| | - Sanatan Majhi
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (02115), United States of America
| | - Kshitij Rb Singh
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu, Kitakyushu (8080196), Japan.
| | - Rout George Kerry
- Department of Biotechnology, Utkal University, Vani Vihar, Bhubaneswar, Odisha (751004), India.
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24
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Mishra S. Emerging Trends in Cryo-EM-based Structural Studies of Neuropathological Amyloids. J Mol Biol 2023; 435:168361. [PMID: 37949311 DOI: 10.1016/j.jmb.2023.168361] [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: 09/29/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Tauopathies, synucleinopathies, Aβ amyloidosis, TDP-43 proteinopathies, and prion diseases- these neurodegenerative diseases have in common the formation of amyloid filaments rich in cross-β sheets. Cryo-electron microscopy now permits the visualization of amyloid assemblies at atomic resolution, ushering a wide range of structural studies on several of these poorly understood amyloidogenic proteins. Amyloids are polymorphic with minor modulations in reaction environment affecting the overall architecture of their assembly, making amyloids an extremely challenging venture for structure-based therapeutic intervention. In 2017, the first cryo-EM structure of tau filaments from an Alzheimer's disease-affected brain established that in vitro assemblies might not necessarily reflect the native amyloid fold. Since then, brain-derived amyloid structures for several proteins across many neurodegenerative diseases have uncovered the disease-relevant amyloid folds. It has now been shown for tauopathies, synucleinopathies and TDP-43 proteinopathies, that distinct amyloid folds of the same protein might be related to different diseases. Salient features of each of these brain-derived folds are discussed in detail. It was also recently observed that seeded aggregation does not necessarily replicate the brain-derived structural fold. Owing to high throughput structure determination, some of these native amyloid folds have also been successfully replicated in vitro. In vitro replication of disease-relevant filaments will aid development of imaging ligands and defibrillating drugs. Towards this direction, recent high-resolution structures of tau filaments with positron emission tomography tracers and a defibrillating drug are also discussed. This review summarizes and celebrates the recent advancements in structural understanding of neuropathological amyloid filaments using cryo-EM.
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Affiliation(s)
- Suman Mishra
- Molecular Biophysics Unit, Biological Sciences Division, Indian Institute of Science, Bengaluru 560 012, Karnataka, India.
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25
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Halder D, Das S, R S J, Joseph A. Role of multi-targeted bioactive natural molecules and their derivatives in the treatment of Alzheimer's disease: an insight into structure-activity relationship. J Biomol Struct Dyn 2023; 41:11286-11323. [PMID: 36579430 DOI: 10.1080/07391102.2022.2158136] [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: 09/13/2022] [Accepted: 12/07/2022] [Indexed: 12/30/2022]
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disorder involving cognitive dysfunction like short-term memory and behavioral changes as the disease progresses due to other unaltered physiological factors. The solution for this problem is Multi-targeted Drugs (MTDs), which can affect multiple determinants to realize the multifunctional effects. Acetylcholinesterase (AChE) inhibitors donepezil, rivastigmine, galantamine, and N-methyl-D-aspartate (NMDA) receptor antagonist memantine are FDA-approved drugs used to treat AD symptomatically. The key objective of this review is to understand multitargeted bioactive natural molecules that could be considered as leads for further development as effective drugs for treating AD, along with understanding its pharmacology and structure-activity relationship (SAR). Understanding the molecular mechanism of the AD pathophysiology, the role of existing drugs, treatment of AD via amyloid beta (Aβ) plaque, and neurofibrillary tangle (NFT) inhibition by natural bioactive molecules were also discussed in the review. The current quest and recent advancements with natural bioactive compounds like physostigmine, resveratrol, curcumin, and catechins, along with the study of in silico SAR, were reported in the present study. This review summarises the structural properties required for bioactive natural molecules to show anti-Alzheimer's activity by emphasizing on SAR of several bioactive natural molecules targeting various AD pathologies, their key molecular interactions that are critical for target specificity, their role as multitargeted ligands, used with adjunctive therapy for AD followed by related US patents granted recently. This article highlights the significance of the structural features of natural bioactive molecules in the treatment of AD and establishes a connection between them.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debojyoti Halder
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Subham Das
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Jeyaprakash R S
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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26
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Fernández Ramírez MDC, Afrin S, Saelices L. Conformational inhibitors of protein aggregation. Curr Opin Struct Biol 2023; 83:102700. [PMID: 37717490 DOI: 10.1016/j.sbi.2023.102700] [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: 07/12/2023] [Revised: 08/16/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023]
Abstract
Amyloidoses are fatal conditions associated with the aggregation of proteins into amyloid fibrils that deposit systemically and/or locally. Possibly because the causal mechanism of protein aggregation and deposition is not fully understood, this group of diseases remains uncurable. Advances in structural biology, such as the use of nuclear magnetic resonance and cryo-electron microscopy, have enabled the study of the structures and the conformational nature of the proteins whose aggregation is associated with the underlying pathogenesis of amyloidosis. As a result, the last years of research have translated into the development of directed therapeutic strategies that target the specific conformations of precursors, fibrils, and intermediary species. Current efforts include the use of small molecules, peptides, and antibodies. This review summarizes the recent progress in developing strategies that target specific protein conformations for the treatment of amyloidoses.
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Affiliation(s)
- María Del Carmen Fernández Ramírez
- Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA. https://twitter.com/FernandezR_MC
| | - Shumaila Afrin
- Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA. https://twitter.com/Shumyla44
| | - Lorena Saelices
- Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr Brain Institute, University of Texas Southwestern Medical Center (UTSW), Dallas, TX, USA.
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27
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Smith MS, Knight IS, Kormos RC, Pepe JG, Kunach P, Diamond MI, Shahmoradian SH, Irwin JJ, DeGrado WF, Shoichet BK. Docking for molecules that bind in a symmetric stack with SymDOCK. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.564400. [PMID: 37961414 PMCID: PMC10634874 DOI: 10.1101/2023.10.27.564400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Discovering ligands for amyloid fibrils, such as those formed by the tau protein, is an area of much current interest. In recent structures, ligands bind in stacks in the tau fibrils to reflect the rotational and translational symmetry of the fibril itself; in these structures the ligands make few interactions with the protein but interact extensively with each other. To exploit this symmetry and stacking, we developed SymDOCK, a method to dock molecules that follow the protein's symmetry. For each prospective ligand pose, we apply the symmetry operation of the fibril to generate a self-interacting and fibril-interacting stack, checking that doing so will not cause a clash between the original molecule and its image. Absent a clash, we retain that pose and add the ligand-ligand van der Waals energy to the ligand's docking score (here using DOCK3.8). We can check these geometries and energies using an implementation of ANI, a neural network-based quantum-mechanical evaluation of the ligand stacking energies. In retrospective calculations, symmetry docking can reproduce the poses of three tau PET tracers whose structures have been determined. More convincingly, in a prospective study SymDOCK predicted the structure of the PET tracer MK-6240 bound in a symmetrical stack to AD PHF tau before that structure was determined; the docked pose was used to determine how MK-6240 fit the cryo-EM density. In proof-of-concept studies, SymDOCK enriched known ligands over property-matched decoys in retrospective screens without sacrificing docking speed, and can address large library screens that seek new symmetrical stackers. Future applications of this approach will be considered.
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Affiliation(s)
- Matthew S. Smith
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Program in Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Ian S. Knight
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Rian C. Kormos
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Program in Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph G. Pepe
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Program in Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Peter Kunach
- McGill Research Centre for Studies in Aging, McGill University, Montreal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Marc I. Diamond
- Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sarah H. Shahmoradian
- Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John J. Irwin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
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28
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Garcia-Pardo J, Ventura S. Chemical targeting of amyloids. Nat Chem Biol 2023; 19:1176-1177. [PMID: 37495777 DOI: 10.1038/s41589-023-01394-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Affiliation(s)
- Javier Garcia-Pardo
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
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29
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Faridi N, Sanjari-Pour M, Wang P, Bathaie SZ. The Effect of Ultrasonication on the Fibrillar/ Oligomeric Structures of Aβ 1-42 at Different Concentrations. Protein J 2023; 42:575-585. [PMID: 37634212 PMCID: PMC10480282 DOI: 10.1007/s10930-023-10138-0] [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] [Accepted: 07/10/2023] [Indexed: 08/29/2023]
Abstract
The number of disease states linked the aberrant regular protein conformations to oligomers and amyloid fibrils. Amyloid beta 1-42 (Aβ1-42) peptide is very hydrophobic and quickly forms the β-rich structure and fibrillar protein aggregates in some solutions and buffer conditions. Ultrasonication pulses can disrupt amyloid fibrils to smaller fragments and produce Aβ1-42 peptides of different sizes and oligomers. Herein, we investigated the effects of buffer and ultrasonication on Aβ1-42 structure at low and high concentrations. After ultrasonication, the Western blot results showed that Aβ1-42 fibrils were disaggregated into different sizes. The transmission electron microscopy results indicated Aβ1-42 at low concentration (25 µM) in Ham's/F12 phenol red-free culture medium formed short-size fragments and oligomers. In comparison, Aβ1-42 at higher concentration (100 µM) formed fibrils that break down into smaller fragments after ultrasonication. However, after regrowth, it formed mature fibrils again. Cell viability assay indicated that Aβ1-42 oligomers formed at a low concentration (25 µM) were more toxic to PC12 cells than other forms. In conclusion, by applying ultrasonication pulses and controlling peptide concentration and buffer condition, we can rich Aβ1-42 aggregates with a particular size and molecular structure.
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Affiliation(s)
- Nassim Faridi
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box. 14115-133, Tehran, Iran
- Institute for Natural Products and Medicinal Plants, Tarbiat Modares University, Tehran, Iran
| | - Maryam Sanjari-Pour
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box. 14115-133, Tehran, Iran
| | - Ping Wang
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - S Zahra Bathaie
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box. 14115-133, Tehran, Iran.
- Institute for Natural Products and Medicinal Plants, Tarbiat Modares University, Tehran, Iran.
- UCLA-DOE Institute, University of California, Los Angeles, CA, USA.
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30
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Kunach P, Vaquer-Alicea J, Smith MS, Hopewell R, Monistrol J, Moquin L, Therriault J, Tissot C, Rahmouni N, Massarweh G, Soucy JP, Guiot MC, Shoichet BK, Rosa-Neto P, Diamond MI, Shahmoradian SH. Cryo-EM structure of Alzheimer's disease tau filaments with PET ligand MK-6240. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.558671. [PMID: 37790438 PMCID: PMC10542181 DOI: 10.1101/2023.09.22.558671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Positron Emission Tomography (PET) ligands have advanced Alzheimer's disease (AD) diagnosis and treatment. Using autoradiography and cryo-EM, we identified AD brain tissue with elevated tau burden, purified filaments, and determined the structure of second-generation high avidity PET ligand MK-6240 at 2.31 Å resolution, which bound at a 1:1 ratio within the cleft of tau paired-helical filament (PHF), engaging with glutamine 351, lysine K353, and isoleucine 360. This information elucidates the basis of MK-6240 PET in quantifying PHF deposits in AD and may facilitate the structure-based design of superior ligands against tau amyloids.
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Affiliation(s)
- Peter Kunach
- Department of Neurology, McGill University, Montreal, Quebec, Canada
- Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, Dallas, TX, United States
| | - Jaime Vaquer-Alicea
- Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, Dallas, TX, United States
| | - Matthew S. Smith
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, United States
- Program of Biophysics, UCSF, San Francisco, CA, United States
| | | | - Jim Monistrol
- Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, Dallas, TX, United States
| | - Luc Moquin
- Montreal Neurological Institute, Montreal, Quebec, Canada
| | - Joseph Therriault
- Department of Neurology, McGill University, Montreal, Quebec, Canada
| | - Cecile Tissot
- Department of Neurology, McGill University, Montreal, Quebec, Canada
| | - Nesrine Rahmouni
- Department of Neurology, McGill University, Montreal, Quebec, Canada
| | | | | | - Marie-Christine Guiot
- Department of Neurology, McGill University, Montreal, Quebec, Canada
- Montreal Neurological Institute, Montreal, Quebec, Canada
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, United States
| | - Pedro Rosa-Neto
- Department of Neurology, McGill University, Montreal, Quebec, Canada
| | - Marc I. Diamond
- Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, Dallas, TX, United States
| | - Sarah H. Shahmoradian
- Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, Dallas, TX, United States
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Scheres SHW, Ryskeldi-Falcon B, Goedert M. Molecular pathology of neurodegenerative diseases by cryo-EM of amyloids. Nature 2023; 621:701-710. [PMID: 37758888 DOI: 10.1038/s41586-023-06437-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/14/2023] [Indexed: 09/29/2023]
Abstract
Abnormal assembly of tau, α-synuclein, TDP-43 and amyloid-β proteins into amyloid filaments defines most human neurodegenerative diseases. Genetics provides a direct link between filament formation and the causes of disease. Developments in cryo-electron microscopy (cryo-EM) have made it possible to determine the atomic structures of amyloids from postmortem human brains. Here we review the structures of brain-derived amyloid filaments that have been determined so far and discuss their impact on research into neurodegeneration. Whereas a given protein can adopt many different filament structures, specific amyloid folds define distinct diseases. Amyloid structures thus provide a description of neuropathology at the atomic level and a basis for studying disease. Future research should focus on model systems that replicate the structures observed in disease to better understand the molecular mechanisms of disease and develop improved diagnostics and therapies.
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Affiliation(s)
- Sjors H W Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | | | - Michel Goedert
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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Naskar A, Nayak A, Salaikumaran MR, Vishal SS, Gopal PP. Phase separation and pathologic transitions of RNP condensates in neurons: implications for amyotrophic lateral sclerosis, frontotemporal dementia and other neurodegenerative disorders. Front Mol Neurosci 2023; 16:1242925. [PMID: 37720552 PMCID: PMC10502346 DOI: 10.3389/fnmol.2023.1242925] [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: 06/20/2023] [Accepted: 08/21/2023] [Indexed: 09/19/2023] Open
Abstract
Liquid-liquid phase separation results in the formation of dynamic biomolecular condensates, also known as membrane-less organelles, that allow for the assembly of functional compartments and higher order structures within cells. Multivalent, reversible interactions between RNA-binding proteins (RBPs), including FUS, TDP-43, and hnRNPA1, and/or RNA (e.g., RBP-RBP, RBP-RNA, RNA-RNA), result in the formation of ribonucleoprotein (RNP) condensates, which are critical for RNA processing, mRNA transport, stability, stress granule assembly, and translation. Stress granules, neuronal transport granules, and processing bodies are examples of cytoplasmic RNP condensates, while the nucleolus and Cajal bodies are representative nuclear RNP condensates. In neurons, RNP condensates promote long-range mRNA transport and local translation in the dendrites and axon, and are essential for spatiotemporal regulation of gene expression, axonal integrity and synaptic function. Mutations of RBPs and/or pathologic mislocalization and aggregation of RBPs are hallmarks of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer's disease. ALS/FTD-linked mutations of RBPs alter the strength and reversibility of multivalent interactions with other RBPs and RNAs, resulting in aberrant phase transitions. These aberrant RNP condensates have detrimental functional consequences on mRNA stability, localization, and translation, and ultimately lead to compromised axonal integrity and synaptic function in disease. Pathogenic protein aggregation is dependent on various factors, and aberrant dynamically arrested RNP condensates may serve as an initial nucleation step for pathologic aggregate formation. Recent studies have focused on identifying mechanisms by which neurons resolve phase transitioned condensates to prevent the formation of pathogenic inclusions/aggregates. The present review focuses on the phase separation of neurodegenerative disease-linked RBPs, physiological functions of RNP condensates, and the pathologic role of aberrant phase transitions in neurodegenerative disease, particularly ALS/FTD. We also examine cellular mechanisms that contribute to the resolution of aberrant condensates in neurons, and potential therapeutic approaches to resolve aberrantly phase transitioned condensates at a molecular level.
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Affiliation(s)
- Aditi Naskar
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
| | - Asima Nayak
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
| | | | - Sonali S. Vishal
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
| | - Pallavi P. Gopal
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale School of Medicine, New Haven, CT, United States
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Bridges LR. Replicating RNA as a component of scrapie fibrils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553578. [PMID: 37645951 PMCID: PMC10462133 DOI: 10.1101/2023.08.17.553578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Recently, electron cryo-microscopy (cryo-EM) maps of fibrils from the brains of mice and hamsters with five infectious scrapie strains have been published1-5 and deposited in the electron microscopy data bank (EMDB)6. This represents long-awaited near-atomic level structural evidence, widely expected to confirm the protein-only prion hypothesis7,8. Instead, the maps reveal a second component, other than protein. The aim of the present study was to identify the nature of this second component, in the published maps1-5, using an in silico approach. Extra densities (EDs) containing this component were continuous, straight, axial, at right angles to protein rungs and within hydrogen-bonding distance of protein, consistent with a role as guide and support in fibril construction. EDs co-located with strips of basic residues, notably lysines, and formed a conspicuous cladding over parts of the N-terminal lobe of the protein. In one ED, there was evidence of a Y-shaped polymer forming two antiparallel chains, consistent with replicating RNA. Although the protein-only prion hypothesis7 is still popular, convincing counter-evidence for an essential role of RNA as a cofactor has amassed in the last 20 years8. The present findings go beyond this in providing evidence for RNA as the genetic element of scrapie. To reflect the monotonous nature of the protein interface, it is suggested that the RNA may be a tandem repeat. This is against the protein-only prion hypothesis and in favour of a more orthodox agent, more akin to a virus. Fibrils from brains of patients with Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) and other neurodegenerations also contain EDs9 and may be of a similar aetiology.
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Affiliation(s)
- Leslie R Bridges
- Neuropathology, Cellular Pathology, South West London Pathology, St George's Hospital, St George's University Hospitals NHS Foundation Trust, London, UK and Molecular and Clinical Sciences Research Institute, St George's University of London, London, UK
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Arar S, Haque MA, Kayed R. Protein aggregation and neurodegenerative disease: Structural outlook for the novel therapeutics. Proteins 2023:10.1002/prot.26561. [PMID: 37530227 PMCID: PMC10834863 DOI: 10.1002/prot.26561] [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: 06/08/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 08/03/2023]
Abstract
Before the controversial approval of humanized monoclonal antibody lecanemab, which binds to the soluble amyloid-β protofibrils, all the treatments available earlier, for Alzheimer's disease (AD) were symptomatic. The researchers are still struggling to find a breakthrough in AD therapeutic medicine, which is partially attributable to lack in understanding of the structural information associated with the intrinsically disordered proteins and amyloids. One of the major challenges in this area of research is to understand the structural diversity of intrinsically disordered proteins under in vitro conditions. Therefore, in this review, we have summarized the in vitro applications of biophysical methods, which are aimed to shed some light on the heterogeneity, pathogenicity, structures and mechanisms of the intrinsically disordered protein aggregates associated with proteinopathies including AD. This review will also rationalize some of the strategies in modulating disease-relevant pathogenic protein entities by small molecules using structural biology approaches and biophysical characterization. We have also highlighted tools and techniques to simulate the in vivo conditions for native and cytotoxic tau/amyloids assemblies, urge new chemical approaches to replicate tau/amyloids assemblies similar to those in vivo conditions, in addition to designing novel potential drugs.
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Affiliation(s)
- Sharif Arar
- Mitchell Center for Neurodegenerative Diseases
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, 77555, USA
- Department of Chemistry, School of Science, The University of Jordan, Amman 11942, Jordan
| | - Md Anzarul Haque
- Mitchell Center for Neurodegenerative Diseases
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, 77555, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, 77555, USA
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Wijekoon N, Gonawala L, Ratnayake P, Dissanayaka P, Gunarathne I, Amaratunga D, Liyanage R, Senanayaka S, Wijesekara S, Gunasekara HH, Vanarsa K, Castillo J, Hathout Y, Dalal A, Steinbusch HW, Hoffman E, Mohan C, de Silva KRD. Integrated genomic, proteomic and cognitive assessment in Duchenne Muscular Dystrophy suggest astrocyte centric pathology. Heliyon 2023; 9:e18530. [PMID: 37593636 PMCID: PMC10432191 DOI: 10.1016/j.heliyon.2023.e18530] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 07/15/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
Introduction Documented Duchenne Muscular Dystrophy (DMD) biomarkers are confined to Caucasians and are poor indicators of cognitive difficulties and neuropsychological alterations. Materials and methods This study correlates serum protein signatures with cognitive performance in DMD patients of South Asian origin. Study included 25 DMD patients aged 6-16 years. Cognitive profiles were assessed by Wechsler Intelligence Scale for Children. Serum proteome profiling of 1317 proteins was performed in eight DMD patients and eight age-matched healthy volunteers. Results Among the several novel observations we report, better cognitive performance in DMD was associated with increased serum levels of MMP9 and FN1 but decreased Siglec-3, C4b, and C3b. Worse cognitive performance was associated with increased serum levels of LDH-H1 and PDGF-BB but reduced GDF-11, MMP12, TPSB2, and G1B. Secondly, better cognitive performance in Processing Speed (PSI) and Perceptual Reasoning (PRI) domains was associated with intact Dp116, Dp140, and Dp71 dystrophin isoforms while better performance in Verbal Comprehension (VCI) and Working Memory (WMI) domains was associated with intact Dp116 and Dp140 isoforms. Finally, functional pathways shared with Alzheimer's Disease (AD) point towards an astrocyte-centric model for DMD. Conclusion Astrocytic dysfunction leading to synaptic dysfunction reported previously in AD may be a common pathogenic mechanism underlying both AD and DMD, linking protein alterations to cognitive impairment. This new insight may pave the path towards novel therapeutic approaches targeting reactive astrocytes.
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Affiliation(s)
- Nalaka Wijekoon
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Lakmal Gonawala
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, The Netherlands
| | | | - Pulasthi Dissanayaka
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | - Isuru Gunarathne
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | | | - Roshan Liyanage
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | | | - Saraji Wijesekara
- Department of Pediatrics, University of Sri Jayewardenepura, 10250, Sri Lanka
- Colombo South Teaching Hospital, 10350, Sri Lanka
| | | | - Kamala Vanarsa
- Department of Bioengineering, University of Houston, Houston, 77204, USA
| | - Jessica Castillo
- Department of Bioengineering, University of Houston, Houston, 77204, USA
| | - Yetrib Hathout
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, New York, USA
| | - Ashwin Dalal
- Diagnostics Division, Center for DNA Fingerprinting and Diagnostics, India
| | - Harry W.M. Steinbusch
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Eric Hoffman
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, New York, USA
| | - Chandra Mohan
- Department of Bioengineering, University of Houston, Houston, 77204, USA
| | - K. Ranil D. de Silva
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, The Netherlands
- Institute for Combinatorial Advanced Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana, 10390, Sri Lanka
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Nikiforova A, Sedov I. Molecular Design of Magnetic Resonance Imaging Agents Binding to Amyloid Deposits. Int J Mol Sci 2023; 24:11152. [PMID: 37446329 DOI: 10.3390/ijms241311152] [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: 06/12/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
The ability to detect and monitor amyloid deposition in the brain using non-invasive imaging techniques provides valuable insights into the early diagnosis and progression of Alzheimer's disease and helps to evaluate the efficacy of potential treatments. Magnetic resonance imaging (MRI) is a widely available technique offering high-spatial-resolution imaging. It can be used to visualize amyloid deposits with the help of amyloid-binding diagnostic agents injected into the body. In recent years, a number of amyloid-targeted MRI probes have been developed, but none of them has entered clinical practice. We review the advances in the field and deduce the requirements for the molecular structure and properties of a diagnostic probe candidate. These requirements make up the base for the rational design of MRI-active small molecules targeting amyloid deposits. Particular attention is paid to the novel cryo-EM structures of the fibril aggregates and their complexes, with known binders offering the possibility to use computational structure-based design methods. With continued research and development, MRI probes may revolutionize the diagnosis and treatment of neurodegenerative diseases, ultimately improving the lives of millions of people worldwide.
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Affiliation(s)
- Alena Nikiforova
- Chemical Institute, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
| | - Igor Sedov
- Chemical Institute, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
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Hurtle BT, Xie L, Donnelly CJ. Disrupting pathologic phase transitions in neurodegeneration. J Clin Invest 2023; 133:e168549. [PMID: 37395272 DOI: 10.1172/jci168549] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023] Open
Abstract
Solid-like protein deposits found in aged and diseased human brains have revealed a relationship between insoluble protein accumulations and the resulting deficits in neurologic function. Clinically diverse neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, frontotemporal lobar degeneration, and amyotrophic lateral sclerosis, exhibit unique and disease-specific biochemical protein signatures and abnormal protein depositions that often correlate with disease pathogenesis. Recent evidence indicates that many pathologic proteins assemble into liquid-like protein phases through the highly coordinated process of liquid-liquid phase separation. Over the last decade, biomolecular phase transitions have emerged as a fundamental mechanism of cellular organization. Liquid-like condensates organize functionally related biomolecules within the cell, and many neuropathology-associated proteins reside within these dynamic structures. Thus, examining biomolecular phase transitions enhances our understanding of the molecular mechanisms mediating toxicity across diverse neurodegenerative diseases. This Review explores the known mechanisms contributing to aberrant protein phase transitions in neurodegenerative diseases, focusing on tau and TDP-43 proteinopathies and outlining potential therapeutic strategies to regulate these pathologic events.
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Affiliation(s)
- Bryan T Hurtle
- Center for Neuroscience at the University of Pittsburgh Graduate Program
- Medical Scientist Training Program, University of Pittsburgh; and
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Longxin Xie
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Christopher J Donnelly
- Center for Neuroscience at the University of Pittsburgh Graduate Program
- Medical Scientist Training Program, University of Pittsburgh; and
- LiveLikeLou Center for ALS Research at the University of Pittsburgh Brain Institute; Pittsburgh, Pennsylvania, USA
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Halder D, Das S, Joseph A. An insight into structure-activity relationship of naturally derived biological macromolecules for the treatment of Alzheimer's disease: a review. J Biomol Struct Dyn 2023:1-17. [PMID: 37378526 DOI: 10.1080/07391102.2023.2230279] [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: 03/14/2023] [Accepted: 06/21/2023] [Indexed: 06/29/2023]
Abstract
Alzheimer's disease (AD) is a neurological disorder that affects millions of people worldwide. There are currently no cures for AD, although various drugs are used to manage the symptoms and reduce the disease's progression. AChE inhibitors such as rivastigmine, donepezil, galantamine, and the NMDA glutamate receptor antagonist memantine are currently FDA-approved drugs used in the treatment of AD. Recently, naturally derived biological macromolecules have shown promising results in the treatment of AD. Several biological macromolecules derived from natural sources are in various stages of preclinical and clinical trials. During the literature search, it was observed that there is a lack of a comprehensive review that particularly focuses on the role of naturally derived biological macromolecules (protein, carbohydrates, lipids, and nucleic acids) in the treatment of AD and the structure-activity relationship (SAR) approach for understanding the medicinal chemistry perspective. This review focuses on the SAR and probable mechanisms of action of biological macromolecules derived from natural sources for the treatment of AD, including peptides, proteins, enzymes, and polysaccharides. The paper further addresses the therapeutic possibilities of monoclonal antibodies, enzymes, and vaccines for the treatment of AD. Overall, the review provides insight into the SAR of naturally derived biological macromolecules in the treatment of AD. The ongoing research in this field holds great promise for the future development of AD treatment and provides hope for individuals affected by this devastating disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debojyoti Halder
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Subham Das
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
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Wang J, Yu Z, Peng Y, Xu B. Insights into prevention mechanisms of bioactive components from healthy diets against Alzheimer's disease. J Nutr Biochem 2023:109397. [PMID: 37301484 DOI: 10.1016/j.jnutbio.2023.109397] [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: 12/26/2022] [Revised: 05/01/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease in which senile plaques, neurofibrillary tangles, insulin resistance, oxidative stress, chronic neuroinflammation, and abnormal neurotransmission are the potential mechanisms involved in its onset and development. Although it is still an intractable disorder, diet intervention has been developed as an innovative strategy for AD prevention. Some bioactive compounds and micronutrients from food, including soy isoflavones, rutin, vitamin B1, etc., have exhibited numerous neuronal health-promoting effects in both in vivo and in vitro studies. It is well known that their antiapoptotic, antioxidative, and anti-inflammatory properties prevent the neuronal or glial cells from injury or death, minimize oxidative damage, inhibit the production of proinflammatory cytokines by modulating typical signaling pathways of MAPK, NF-kβ, and TLR, and further reduce Aβ genesis and tau hyperphosphorylation. However, parts of the dietary components trigger AD-related proteins productions and inflammasome as well as inflammatory gene upregulation. This review summarized the neuroprotective or nerve damage-promoting role and underlying molecular mechanisms of flavonoids, vitamins, and fatty acids via the data from library databases, PubMed, and journal websites, which provides a comprehensive analysis of the prevention potential of these dietary components against AD.
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Affiliation(s)
- Jingwen Wang
- Food Science and Technology Program, Department of Life Sciences, BNU-HKBU United International College, Zhuhai, Guangdong 519087, China
| | - Zhiling Yu
- Centre for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Ye Peng
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Baojun Xu
- Food Science and Technology Program, Department of Life Sciences, BNU-HKBU United International College, Zhuhai, Guangdong 519087, China.
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Pinzi L, Bisi N, Sorbi C, Franchini S, Tonali N, Rastelli G. Insights into the Structural Conformations of the Tau Protein in Different Aggregation Status. Molecules 2023; 28:molecules28114544. [PMID: 37299020 DOI: 10.3390/molecules28114544] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/23/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Tau is a protein characterized by large structural portions displaying extended conformational changes. Unfortunately, the accumulation of this protein into toxic aggregates in neuronal cells leads to a number of severe pathologies, collectively named tauopathies. In the last decade, significant research advancements were achieved, including a better understanding of Tau structures and their implication in different tauopathies. Interestingly, Tau is characterized by a high structural variability depending on the type of disease, the crystallization conditions, and the formation of pathologic aggregates obtained from in vitro versus ex vivo samples. In this review, we reported an up-to-date and comprehensive overview of Tau structures reported in the Protein Data Bank, with a special focus on discussing the connections between structural features, different tauopathies, different crystallization conditions, and the use of in vitro or ex vivo samples. The information reported in this article highlights very interesting links between all these aspects, which we believe may be of particular relevance for a more informed structure-based design of compounds able to modulate Tau aggregation.
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Affiliation(s)
- Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy
| | - Nicolò Bisi
- Centre National de la Recherche Scientifique (CNRS), Université de Paris-Saclay, BioCIS, Bat. Henri Moissan, 17 Av. des Sciences, 91400 Orsay, France
| | - Claudia Sorbi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy
| | - Silvia Franchini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy
| | - Nicolò Tonali
- Centre National de la Recherche Scientifique (CNRS), Université de Paris-Saclay, BioCIS, Bat. Henri Moissan, 17 Av. des Sciences, 91400 Orsay, France
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy
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Majid N, Khan RH. Protein aggregation: Consequences, mechanism, characterization and inhibitory strategies. Int J Biol Macromol 2023; 242:125123. [PMID: 37270122 DOI: 10.1016/j.ijbiomac.2023.125123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/01/2023] [Accepted: 05/25/2023] [Indexed: 06/05/2023]
Abstract
Proteins play a major role in the regulation of various cellular functions including the synthesis of structural components. But proteins are stable under physiological conditions only. A slight variation in environmental conditions can cost them huge in terms of conformational stability ultimately leading to aggregation. Under normal conditions, aggregated proteins are degraded or removed from the cell by a quality control system including ubiquitin-proteasomal machinery and autophagy. But they are burdened under diseased conditions or are impaired by the aggregated proteins leading to the generation of toxicity. The misfolding and aggregation of protein such as amyloid-β, α-synuclein, human lysozyme etc., are responsible for certain diseases including Alzheimer, Parkinson, and non- neuropathic systemic amyloidosis respectively. Extensive research has been done to find the therapeutics for such diseases but till now we have got only symptomatic treatment that will reduce the disease severity but will not target the initial formation of nucleus responsible for disease progression and propagation. Hence there is an urgent need to develop the drugs targeting the cause of the disease. For this, a wide knowledge related to misfolding and aggregation under the same heading is required as described in this review alongwith the strategies hypothesized and implemented till now. This will contribute a lot to the work of researchers in the field of neuroscience.
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Affiliation(s)
- Nabeela Majid
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
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Shi Y, Ghetti B, Goedert M, Scheres SHW. Cryo-EM Structures of Chronic Traumatic Encephalopathy Tau Filaments with PET Ligand Flortaucipir. J Mol Biol 2023; 435:168025. [PMID: 37330290 PMCID: PMC7615338 DOI: 10.1016/j.jmb.2023.168025] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Positron emission tomography (PET) imaging allows monitoring the progression of amyloid aggregation in the living brain. [18F]-Flortaucipir is the only approved PET tracer compound for the visualisation of tau aggregation. Here, we describe cryo-EM experiments on tau filaments in the presence and absence of flortaucipir. We used tau filaments isolated from the brain of an individual with Alzheimer's disease (AD), and from the brain of an individual with primary age-related tauopathy (PART) with a co-pathology of chronic traumatic encephalopathy (CTE). Unexpectedly, we were unable to visualise additional cryo-EM density for flortaucipir for AD paired helical or straight filaments (PHFs or SFs), but we did observe density for flortaucipir binding to CTE Type I filaments from the case with PART. In the latter, flortaucipir binds in a 1:1 molecular stoichiometry with tau, adjacent to lysine 353 and aspartate 358. By adopting a tilted geometry with respect to the helical axis, the 4.7 Å distance between neighbouring tau monomers is reconciled with the 3.5 Å distance consistent with π-π-stacking between neighbouring molecules of flortaucipir.
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Affiliation(s)
- Yang Shi
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA. https://twitter.com/GhettiBernardi1
| | - Michel Goedert
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Sjors H W Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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Sun R, Zhang S, Liu Y, Li D. Chemical probes for investigating protein liquid-liquid phase separation and aggregation. Curr Opin Chem Biol 2023; 74:102291. [PMID: 37004350 DOI: 10.1016/j.cbpa.2023.102291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/22/2023] [Accepted: 02/26/2023] [Indexed: 04/03/2023]
Abstract
Protein liquid-liquid phase separation drives the dynamic assembly of membraneless organelles for fulfilling different physiological functions. Under diseased condition, protein may undergo liquid-to-solid condensation to form pathological amyloid aggregates closely associated with neurodegenerative diseases. Chemical probe serves as an important chemical tool not only for exploring the basic principle of the dynamic assembly of different protein condensates in vitro and in cell but also for clinical diagnosis and therapeutics of the related diseases. In this review, we first introduce chemical probes to image and regulate protein condensates. Then, we summarized three different categories of chemical probes including general amyloid dye, selective positron emission tomography tracer, and disaggregating binder, which feature distinct interaction pattern and activity upon binding to different pathological amyloid fibrillar aggregates. Next, we discuss the development of chemical probes for tracking protein amorphous aggregates in cells. Finally, we point out future direction in expanding the probes' chemical space and applications.
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Affiliation(s)
- Rui Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Shenqing Zhang
- Bio-X-Renji Hospital Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China; Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China.
| | - Dan Li
- Bio-X-Renji Hospital Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China; Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, World Laureates Association, Shanghai 201203, China.
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44
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Walton-Raaby M, Woods R, Kalyaanamoorthy S. Investigating the Theranostic Potential of Graphene Quantum Dots in Alzheimer's Disease. Int J Mol Sci 2023; 24:ijms24119476. [PMID: 37298426 DOI: 10.3390/ijms24119476] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/16/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Alzheimer's disease (AD) is one of the leading causes of death worldwide, with no definitive diagnosis or known cure. The aggregation of Tau protein into neurofibrillary tangles (NFTs), which contain straight filaments (SFs) and paired helical filaments (PHFs), is a major hallmark of AD. Graphene quantum dots (GQDs) are a type of nanomaterial that combat many of the small-molecule therapeutic challenges in AD and have shown promise in similar pathologies. In this study, two sizes of GQDs, GQD7 and GQD28, were docked to various forms of Tau monomers, SFs, and PHFs. From the favorable docked poses, we simulated each system for at least 300 ns and calculated the free energies of binding. We observed a clear preference for GQD28 in the PHF6 (306VQIVYK311) pathological hexapeptide region of monomeric Tau, while GQD7 targeted both the PHF6 and PHF6* (275VQIINK280) pathological hexapeptide regions. In SFs, GQD28 had a high affinity for a binding site that is available in AD but not in other common tauopathies, while GQD7 behaved promiscuously. In PHFs, GQD28 interacted strongly near the protofibril interface at the putative disaggregation site for epigallocatechin-3-gallate, and GQD7 largely interacted with PHF6. Our analyses revealed several key GQD binding sites that may be used for detecting, preventing, and disassembling the Tau aggregates in AD.
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Affiliation(s)
- Max Walton-Raaby
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Riley Woods
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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45
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Merz GE, Chalkley MJ, Tan SK, Tse E, Lee J, Prusiner SB, Paras NA, DeGrado WF, Southworth DR. Stacked binding of a PET ligand to Alzheimer's tau paired helical filaments. Nat Commun 2023; 14:3048. [PMID: 37236970 PMCID: PMC10220082 DOI: 10.1038/s41467-023-38537-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Accumulation of filamentous aggregates of tau protein in the brain is a pathological hallmark of Alzheimer's disease (AD) and many other neurodegenerative tauopathies. The filaments adopt disease-specific cross-β amyloid conformations that self-propagate and are implicated in neuronal loss. Development of molecular diagnostics and therapeutics is of critical importance. However, mechanisms of small molecule binding to the amyloid core is poorly understood. We used cryo-electron microscopy to determine a 2.7 Å structure of AD patient-derived tau paired-helical filaments bound to the PET ligand GTP-1. The compound is bound stoichiometrically at a single site along an exposed cleft of each protofilament in a stacked arrangement matching the fibril symmetry. Multiscale modeling reveals pi-pi aromatic interactions that pair favorably with the small molecule-protein contacts, supporting high specificity and affinity for the AD tau conformation. This binding mode offers critical insight into designing compounds to target different amyloid folds found across neurodegenerative diseases.
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Affiliation(s)
- Gregory E Merz
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Matthew J Chalkley
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Sophia K Tan
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Eric Tse
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Joanne Lee
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Stanley B Prusiner
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Nick A Paras
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - William F DeGrado
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Daniel R Southworth
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
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46
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Indig RY, Landau M. Designed inhibitors to reduce amyloid virulence and cytotoxicity and combat neurodegenerative and infectious diseases. Curr Opin Chem Biol 2023; 75:102318. [PMID: 37196450 DOI: 10.1016/j.cbpa.2023.102318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 05/19/2023]
Abstract
The review highlights the role of amyloids in various diseases and the challenges associated with targeting human amyloids in therapeutic development. However, due to the better understanding of microbial amyloids' role as virulence factors, there is a growing interest in repurposing and designing anti-amyloid compounds for antivirulence therapy. The identification of amyloid inhibitors has not only significant clinical implications but also provides valuable insights into the structure and function of amyloids. The review showcases small molecules and peptides that specifically target amyloids in both humans and microbes, reducing cytotoxicity and biofilm formation, respectively. The review emphasizes the importance of further research on amyloid structures, mechanisms, and interactions across all life forms to yield new drug targets and improve the design of selective treatments. Overall, the review highlights the potential for amyloid inhibitors in therapeutic development for both human diseases and microbial infections.
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Affiliation(s)
- Rinat Yona Indig
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; Centre for Structural Systems Biology (CSSB) and Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany; Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany; European Molecular Biology Laboratory (EMBL), Hamburg, Germany.
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47
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Tse A, Janilkarn-Urena I, Lin J, Chang X, Efthymiou C, Idrissova A, Zhang M, Williams CK, Magaki S, Vinters HV, Davies DL, Gonen T, Gukasyan HJ, Seidler PM. Improving the solubility of pseudo-hydrophobic Alzheimer's Disease medicinal chemicals through co-crystal formulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538327. [PMID: 37162961 PMCID: PMC10168350 DOI: 10.1101/2023.04.25.538327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Natural products are ligands and potential inhibitors of Alzheimer's disease (AD) tau. Dihydromyricetin (DHM) is a CNS active natural product. Despite having signature polyphenolic character, DHM is ostensibly hydrophobic owing to intermolecular hydrogen bonds that shield hydrophilic phenols. Our research shows DHM becomes ionized at near-neutral pH allowing formulation of salts with transformed solubility. The MicroED co-crystal structure with trolamine reveals DHM salts as metastable solids with unlocked hydrogen bonding and a thermodynamic bent to solubilize in water. All salt formulations show better inhibitory activity against AD tau than the non-salt form, with efficacies correlating to enhanced solubilities. These results underscore the role of structural chemistry in guiding selection of solubilizing agents for chemical formulation. We propose DHM salts are appropriate formulations for research as dietary supplements to promote healthy aging by combating protein misfolding. Additionally, DHM is a suitable lead for medicinal chemistry and possible development of CNS pharmaceuticals.
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Affiliation(s)
- A Tse
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Mann School of Pharmacy and Pharmaceutical Sciences, 1985 Zonal Ave, Los Angeles, CA 90089-9121, USA
- Authors contributed equally to experimental work
| | - I Janilkarn-Urena
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Mann School of Pharmacy and Pharmaceutical Sciences, 1985 Zonal Ave, Los Angeles, CA 90089-9121, USA
- Authors contributed equally to experimental work
| | - J Lin
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, David Geffen School of Medicine at University of California, Los Angeles, California 90095
- Authors contributed equally to experimental work
| | - X Chang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Mann School of Pharmacy and Pharmaceutical Sciences, 1985 Zonal Ave, Los Angeles, CA 90089-9121, USA
| | - C Efthymiou
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Mann School of Pharmacy and Pharmaceutical Sciences, 1985 Zonal Ave, Los Angeles, CA 90089-9121, USA
| | - A Idrissova
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Mann School of Pharmacy and Pharmaceutical Sciences, 1985 Zonal Ave, Los Angeles, CA 90089-9121, USA
| | - M Zhang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Mann School of Pharmacy and Pharmaceutical Sciences, 1985 Zonal Ave, Los Angeles, CA 90089-9121, USA
| | - CK Williams
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, California 90095
| | - S Magaki
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, California 90095
| | - HV Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, California 90095
- Department of Neurology, David Geffen School of Medicine at University of California, Los Angeles, California 90095
| | - DL Davies
- Titus Family Department of Clinical Pharmacy, University of Southern California School of Pharmacy, Los Angeles, CA 90089, USA
| | - T Gonen
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - HJ Gukasyan
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Mann School of Pharmacy and Pharmaceutical Sciences, 1985 Zonal Ave, Los Angeles, CA 90089-9121, USA
| | - PM Seidler
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Mann School of Pharmacy and Pharmaceutical Sciences, 1985 Zonal Ave, Los Angeles, CA 90089-9121, USA
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48
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Im D, Kim S, Yoon G, Hyun DG, Eom YG, Lee YE, Sohn CH, Choi JM, Kim HI. Decoding the Roles of Amyloid-β (1-42)'s Key Oligomerization Domains toward Designing Epitope-Specific Aggregation Inhibitors. JACS AU 2023; 3:1065-1075. [PMID: 37124297 PMCID: PMC10131210 DOI: 10.1021/jacsau.2c00668] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 05/03/2023]
Abstract
Fibrillar amyloid aggregates are the pathological hallmarks of multiple neurodegenerative diseases. The amyloid-β (1-42) protein, in particular, is a major component of senile plaques in the brains of patients with Alzheimer's disease and a primary target for disease treatment. Determining the essential domains of amyloid-β (1-42) that facilitate its oligomerization is critical for the development of aggregation inhibitors as potential therapeutic agents. In this study, we identified three key hydrophobic sites (17LVF19, 32IGL34, and 41IA42) on amyloid-β (1-42) and investigated their involvement in the self-assembly process of the protein. Based on these findings, we designed candidate inhibitor peptides of amyloid-β (1-42) aggregation. Using the designed peptides, we characterized the roles of the three hydrophobic regions during amyloid-β (1-42) fibrillar aggregation and monitored the consequent effects on its aggregation property and structural conversion. Furthermore, we used an amyloid-β (1-42) double point mutant (I41N/A42N) to examine the interactions between the two C-terminal end residues with the two hydrophobic regions and their roles in amyloid self-assembly. Our results indicate that interchain interactions in the central hydrophobic region (17LVF19) of amyloid-β (1-42) are important for fibrillar aggregation, and its interaction with other domains is associated with the accessibility of the central hydrophobic region for initiating the oligomerization process. Our study provides mechanistic insights into the self-assembly of amyloid-β (1-42) and highlights key structural domains that facilitate this process. Our results can be further applied toward improving the rational design of candidate amyloid-β (1-42) aggregation inhibitors.
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Affiliation(s)
- Dongjoon Im
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Center
for Proteogenome Research, Korea University, Seoul 02841, Republic of Korea
- Single
Cell Analysis Laboratory, Korea University, Seoul 02841, Republic of Korea
| | - Soohyeong Kim
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Center
for Proteogenome Research, Korea University, Seoul 02841, Republic of Korea
- Single
Cell Analysis Laboratory, Korea University, Seoul 02841, Republic of Korea
| | - Gyusub Yoon
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Center
for Proteogenome Research, Korea University, Seoul 02841, Republic of Korea
- Single
Cell Analysis Laboratory, Korea University, Seoul 02841, Republic of Korea
| | - Da Gyeong Hyun
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Center
for Proteogenome Research, Korea University, Seoul 02841, Republic of Korea
- Single
Cell Analysis Laboratory, Korea University, Seoul 02841, Republic of Korea
| | - Yu-Gon Eom
- Department
of Chemistry, Pusan National University, Busan 46241, Republic of Korea
| | - Ye Eun Lee
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Chang Ho Sohn
- Center
for Nanomedicine, Institute for Basic Science
(IBS), Seoul 03722, Republic of Korea
- Graduate
Program in Nanobiomedical Engineering, Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
| | - Jeong-Mo Choi
- Department
of Chemistry, Pusan National University, Busan 46241, Republic of Korea
- Chemistry
Institute for Functional Materials, Pusan
National University, Busan 46241, Republic
of Korea
| | - Hugh I. Kim
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Center
for Proteogenome Research, Korea University, Seoul 02841, Republic of Korea
- Single
Cell Analysis Laboratory, Korea University, Seoul 02841, Republic of Korea
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49
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Yuan N, Ye L, Sun Y, Wu H, Xiao Z, Fu W, Chen Z, Pei Y, Min Y, Wang D. Molecular Integrative Analysis of the Inhibitory Effects of Dipeptides on Amyloid β Peptide 1-42 Polymerization. Int J Mol Sci 2023; 24:ijms24087673. [PMID: 37108834 PMCID: PMC10141046 DOI: 10.3390/ijms24087673] [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: 03/04/2023] [Revised: 04/02/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
The major pathological feature of Alzheimer's disease (AD) is the aggregation of amyloid β peptide (Aβ) in the brain. Inhibition of Aβ42 aggregation may prevent the advancement of AD. This study employed molecular dynamics, molecular docking, electron microscopy, circular dichroism, staining of aggregated Aβ with ThT, cell viability, and flow cytometry for the detection of reactive oxygen species (ROS) and apoptosis. Aβ42 polymerizes into fibrils due to hydrophobic interactions to minimize free energy, adopting a β-strand structure and forming three hydrophobic areas. Eight dipeptides were screened by molecular docking from a structural database of 20 L-α-amino acids, and the docking was validated by molecular dynamics (MD) analysis of binding stability and interaction potential energy. Among the dipeptides, arginine dipeptide (RR) inhibited Aβ42 aggregation the most. The ThT assay and EM revealed that RR reduced Aβ42 aggregation, whereas the circular dichroism spectroscopy analysis showed a 62.8% decrease in β-sheet conformation and a 39.3% increase in random coiling of Aβ42 in the presence of RR. RR also significantly reduced the toxicity of Aβ42 secreted by SH-SY5Y cells, including cell death, ROS production, and apoptosis. The formation of three hydrophobic regions and polymerization of Aβ42 reduced the Gibbs free energy, and RR was the most effective dipeptide at interfering with polymerization.
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Affiliation(s)
- Nan Yuan
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Lianmeng Ye
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Yan Sun
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Hao Wu
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Zhengpan Xiao
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Wanmeng Fu
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Zuqian Chen
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Yechun Pei
- One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Department of Biosciences, School of Life Sciences, Hainan University, Haikou 570228, China
| | - Yi Min
- Department of Biosciences, School of Life Sciences, Hainan University, Haikou 570228, China
| | - Dayong Wang
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Key Laboratory of Tropical Biological Resources of the Ministry of China, Hainan University, Haikou 570228, China
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50
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Dervişoğlu R, Antonschmidt L, Nimerovsky E, Sant V, Kim M, Ryazanov S, Leonov A, Carlos Fuentes-Monteverde J, Wegstroth M, Giller K, Mathies G, Giese A, Becker S, Griesinger C, Andreas LB. Anle138b interaction in α-synuclein aggregates by dynamic nuclear polarization NMR. Methods 2023; 214:18-27. [PMID: 37037308 DOI: 10.1016/j.ymeth.2023.04.002] [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: 11/30/2022] [Revised: 03/22/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
Small molecules that bind to oligomeric protein species such as membrane proteins and fibrils are of clinical interest for development of therapeutics and diagnostics. Definition of the binding site at atomic resolution via NMR is often challenging due to low binding stoichiometry of the small molecule. For fibrils and aggregation intermediates grown in the presence of lipids, we report atomic-resolution contacts to the small molecule at sub nm distance via solid-state NMR using dynamic nuclear polarization (DNP) and orthogonally labelled samples of the protein and the small molecule. We apply this approach to α-synuclein (αS) aggregates in complex with the small molecule anle138b, which is a clinical drug candidate for disease modifying therapy. The small central pyrazole moiety of anle138b is detected in close proximity to the protein backbone and differences in the contacts between fibrils and early intermediates are observed. For intermediate species, the 100 K condition for DNP helps to preserve the aggregation state, while for both fibrils and oligomers, the DNP enhancement is essential to obtain sufficient sensitivity.
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Affiliation(s)
- Rıza Dervişoğlu
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Leif Antonschmidt
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Evgeny Nimerovsky
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Vrinda Sant
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Myeongkyu Kim
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Sergey Ryazanov
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Center for Neuropathology and Prion Research, Ludwig-Maximilians University, Munich, Germany
| | - Andrei Leonov
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Center for Neuropathology and Prion Research, Ludwig-Maximilians University, Munich, Germany
| | | | - Melanie Wegstroth
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Karin Giller
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | | | - Armin Giese
- Center for Neuropathology and Prion Research, Ludwig-Maximilians University, Munich, Germany
| | - Stefan Becker
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Loren B Andreas
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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