1
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Chakrabarti KS, Bakhtiari D, Rezaei-Ghaleh N. Bifurcations in coupled amyloid-β aggregation-inflammation systems. NPJ Syst Biol Appl 2024; 10:80. [PMID: 39080352 PMCID: PMC11289389 DOI: 10.1038/s41540-024-00408-7] [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: 03/27/2024] [Accepted: 07/23/2024] [Indexed: 08/02/2024] Open
Abstract
A complex interplay between various processes underlies the neuropathology of Alzheimer's disease (AD) and its progressive course. Several lines of evidence point to the coupling between Aβ aggregation and neuroinflammation and its role in maintaining brain homeostasis during the long prodromal phase of AD. Little is however known about how this protective mechanism fails and as a result, an irreversible and progressive transition to clinical AD occurs. Here, we introduce a minimal model of a coupled system of Aβ aggregation and inflammation, numerically simulate its dynamical behavior, and analyze its bifurcation properties. The introduced model represents the following events: generation of Aβ monomers, aggregation of Aβ monomers into oligomers and fibrils, induction of inflammation by Aβ aggregates, and clearance of various Aβ species. Crucially, the rates of Aβ generation and clearance are modulated by inflammation level following a Hill-type response function. Despite its relative simplicity, the model exhibits enormously rich dynamics ranging from overdamped kinetics to sustained oscillations. We then specify the region of inflammation- and coupling-related parameters space where a transition to oscillatory dynamics occurs and demonstrate how changes in Aβ aggregation parameters could shift this oscillatory region in parameter space. Our results reveal the propensity of coupled Aβ aggregation-inflammation systems to oscillatory dynamics and propose prolonged sustained oscillations and their consequent immune system exhaustion as a potential mechanism underlying the transition to a more progressive phase of amyloid pathology in AD. The implications of our results in regard to early diagnosis of AD and anti-AD drug development are discussed.
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Affiliation(s)
- Kalyan S Chakrabarti
- Department of Biological Science and Chemistry, Krea University, Sri City, India
| | | | - Nasrollah Rezaei-Ghaleh
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Düsseldorf, Germany.
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany.
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2
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Leimu L, Holm P, Gąciarz A, Haavisto O, Prince S, Pesonen U, Huovinen T, Lamminmäki U. Epitope-specific antibody fragments block aggregation of AGelD187N, an aberrant peptide in gelsolin amyloidosis. J Biol Chem 2024; 300:107507. [PMID: 38944121 DOI: 10.1016/j.jbc.2024.107507] [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: 04/26/2024] [Revised: 06/10/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
Aggregation of aberrant fragment of plasma gelsolin, AGelD187N, is a crucial event underlying the pathophysiology of Finnish gelsolin amyloidosis, an inherited form of systemic amyloidosis. The amyloidogenic gelsolin fragment AGelD187N does not play any physiological role in the body, unlike most aggregating proteins related to other protein misfolding diseases. However, no therapeutic agents that specifically and effectively target and neutralize AGelD187N exist. We used phage display technology to identify novel single-chain variable fragments that bind to different epitopes in the monomeric AGelD187N that were further maturated by variable domain shuffling and converted to antigen-binding fragment (Fab) antibodies. The generated antibody fragments had nanomolar binding affinity for full-length AGelD187N, as evaluated by biolayer interferometry. Importantly, all four Fabs selected for functional studies efficiently inhibited the amyloid formation of full-length AGelD187N as examined by thioflavin fluorescence assay and transmission electron microscopy. Two Fabs, neither of which bound to the previously proposed fibril-forming region of AGelD187N, completely blocked the amyloid formation of AGelD187N. Moreover, no small soluble aggregates, which are considered pathogenic species in protein misfolding diseases, were formed after successful inhibition of amyloid formation by the most promising aggregation inhibitor, as investigated by size-exclusion chromatography combined with multiangle light scattering. We conclude that all regions of the full-length AGelD187N are important in modulating its assembly into fibrils and that the discovered epitope-specific anti-AGelD187N antibody fragments provide a promising starting point for a disease-modifying therapy for gelsolin amyloidosis, which is currently lacking.
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Affiliation(s)
- Laura Leimu
- R&D, Orion Pharma, Orion Corporation, Turku, Finland; Faculty of Medicine, Institute of Biomedicine, University of Turku, Turku, Finland.
| | - Patrik Holm
- R&D, Orion Pharma, Orion Corporation, Turku, Finland; Department of Life Technologies, University of Turku, Turku, Finland; Organon R&D Finland, Turku, Finland
| | - Anna Gąciarz
- R&D, Orion Pharma, Orion Corporation, Turku, Finland; Mobidiag, A Hologic Company, Espoo, Finland
| | - Oskar Haavisto
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Stuart Prince
- R&D, Orion Pharma, Orion Corporation, Turku, Finland; MediCity Research Laboratory, University of Turku, Turku, Finland
| | - Ullamari Pesonen
- Faculty of Medicine, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Tuomas Huovinen
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Urpo Lamminmäki
- Department of Life Technologies, University of Turku, Turku, Finland.
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3
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Gialama D, Vadukul DM, Thrush RJ, Radford SE, Aprile FA. A Potent Sybody Selectively Inhibits α-Synuclein Amyloid Formation by Binding to the P1 Region. J Med Chem 2024; 67:9857-9868. [PMID: 38842931 PMCID: PMC11215725 DOI: 10.1021/acs.jmedchem.3c02408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/25/2024] [Accepted: 05/17/2024] [Indexed: 06/07/2024]
Abstract
Increasing research efforts focus on exploiting antibodies to inhibit the amyloid formation of neurodegenerative proteins. Nevertheless, it is challenging to discover antibodies that inhibit this process in a specific manner. Using ribosome display, we screened for synthetic single-domain antibodies, i.e., sybodies, of the P1 region of α-synuclein (residues 36-42), a protein that forms amyloid in Parkinson's disease and multiple-system atrophy. Hits were assessed for direct binding to a P1 peptide and the inhibition of amyloid formation. We discovered a sybody, named αSP1, that inhibits amyloid formation of α-synuclein at substoichiometric concentrations in a specific manner, even within highly crowded heterogeneous mixtures. Fluorescence resonance energy transfer-based binding assays and seeding experiments with and without αSP1 further demonstrate the importance of the P1 region for both primary and secondary nucleation mechanisms of amyloid assembly.
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Affiliation(s)
- Dimitra Gialama
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
| | - Devkee M. Vadukul
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
| | - Rebecca J. Thrush
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
- Institute
of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
| | - Sheena E. Radford
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Francesco A. Aprile
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
- Institute
of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
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4
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Masroor A, Zaidi N, Nabi F, Malik S, Zehra S, Arjmand F, Naseem N, Khan RH. Biophysical insight into anti-amyloidogenic nature of novel ionic Co(II)(phen)(H 2O) 4] +[glycinate] - chemotherapeutic drug candidate against human lysozyme aggregation. Biophys Chem 2024; 308:107214. [PMID: 38428228 DOI: 10.1016/j.bpc.2024.107214] [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: 11/21/2023] [Revised: 02/10/2024] [Accepted: 02/25/2024] [Indexed: 03/03/2024]
Abstract
In the recent past, there has been an ever-increasing interest in the search for metal-based therapeutic drug candidates for protein misfolding disorders (PMDs) particularly neurodegenerative disorders such as Alzheimer's, Parkinson's, Prion's diseases, and amyotrophic lateral sclerosis. Also, different amyloidogenic variants of human lysozyme (HL) are involved in hereditary systemic amyloidosis. Metallo-therapeutic agents are extensively studied as antitumor agents, however, they are relatively unexplored for the treatment of non-neuropathic amyloidoses. In this work, inhibition potential of a novel ionic cobalt(II) therapeutic agent (CoTA) of the formulation [Co(phen)(H2O)4]+[glycinate]- is evaluated against HL fibrillation. Various biophysical techniques viz., dye-binding assays, dynamic light scattering (DLS), differential scanning calorimetry (DSC), electron microscopy, and molecular docking experiments validate the proposed mechanism of inhibition of HL fibrillation by CoTA. The experimental corroborative results of these studies reveal that CoTA can suppress and slow down HL fibrillation at physiological temperature and pH. DLS and 1-anilino-8-naphthalenesulfonate (ANS) assay show that reduced fibrillation in the presence of CoTA is marked by a significant decrease in the size and hydrophobicity of the aggregates. Fluorescence quenching and molecular docking results demonstrate that CoTA binds moderately to the aggregation-prone region of HL (Kb = 6.6 × 104 M-1), thereby, inhibiting HL fibrillation. In addition, far-UV CD and DSC show that binding of CoTA to HL does not cause any change in the stability of HL. More importantly, CoTA attenuates membrane damaging effects of HL aggregates against RBCs. This study identifies inorganic metal complexes as a therapeutic intervention for systemic amyloidosis.
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Affiliation(s)
- Aiman Masroor
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P 202002, India
| | - Nida Zaidi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P 202002, India
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P 202002, India
| | - Sadia Malik
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P 202002, India
| | - Siffeen Zehra
- Department of Chemistry, Aligarh Muslim University, Aligarh, U.P 202002, India
| | - Farukh Arjmand
- Department of Chemistry, Aligarh Muslim University, Aligarh, U.P 202002, India
| | - Nida Naseem
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P 202002, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P 202002, India.
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5
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Wang J, Chen S, Yuan Q, Chen J, Li D, Wang L, Yang Y. Predicting the effects of mutations on protein solubility using graph convolution network and protein language model representation. J Comput Chem 2024; 45:436-445. [PMID: 37933773 DOI: 10.1002/jcc.27249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/11/2023] [Accepted: 10/21/2023] [Indexed: 11/08/2023]
Abstract
Solubility is one of the most important properties of protein. Protein solubility can be greatly changed by single amino acid mutations and the reduced protein solubility could lead to diseases. Since experimental methods to determine solubility are time-consuming and expensive, in-silico methods have been developed to predict the protein solubility changes caused by mutations mostly through protein evolution information. However, these methods are slow since it takes long time to obtain evolution information through multiple sequence alignment. In addition, these methods are of low performance because they do not fully utilize protein 3D structures due to a lack of experimental structures for most proteins. Here, we proposed a sequence-based method DeepMutSol to predict solubility change from residual mutations based on the Graph Convolutional Neural Network (GCN), where the protein graph was initiated according to predicted protein structure from Alphafold2, and the nodes (residues) were represented by protein language embeddings. To circumvent the small data of solubility changes, we further pretrained the model over absolute protein solubility. DeepMutSol was shown to outperform state-of-the-art methods in benchmark tests. In addition, we applied the method to clinically relevant genes from the ClinVar database and the predicted solubility changes were shown able to separate pathogenic mutations. All of the data sets and the source code are available at https://github.com/biomed-AI/DeepMutSol.
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Affiliation(s)
- Jing Wang
- Guangzhou institute of technology, Xidian University, Guangzhou, China
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Sheng Chen
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Qianmu Yuan
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Jianwen Chen
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Danping Li
- School of Telecommunications Engineering, Xidian University, Xi'an, China
| | - Lei Wang
- School of Electronic Engineering, Xidian University, Xi'an, China
| | - Yuedong Yang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
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6
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Khursheed A, Viles JH. Impact of Membrane Phospholipids and Exosomes on the Kinetics of Amyloid-β Fibril Assembly. J Mol Biol 2024; 436:168464. [PMID: 38311235 DOI: 10.1016/j.jmb.2024.168464] [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: 12/07/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/10/2024]
Abstract
Alzheimer's disease (AD) is linked with the self-association of the amyloid-β peptide (Aβ) into oligomers and fibrils. The brain is a lipid rich environment for Aβ to assemble, while the brain membrane composition varies in an age dependent manner, we have therefore monitored the influence of lipid bilayer composition on the kinetics of Aβ40 fibril assembly. Using global-fitting models of fibril formation kinetics, we show that the microscopic rate constant for primary nucleation is influenced by variations in phospholipid composition. Anionic phospholipids and particularly those with smaller headgroups shorten fibril formation lag-times, while zwitterionic phospholipids tend to extend them. Using a physiological vesicle model, we show cellular derived exosomes accelerate Aβ40 and Aβ42 fibril formation. Two distinct effects are observed, the presence of even small amounts of any phospholipid will impact the slope of the fibril growth curve. While subsequent additions of phospholipids only affect primary nucleation with the associated change in lag-times. Heightened anionic phospholipids and cholesterol levels are associated with aging and AD respectively, both these membrane components strongly accelerate primary nucleation during Aβ assembly, making a link between disrupted lipid metabolism and Alzheimer's disease.
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Affiliation(s)
- Anum Khursheed
- School of Biological and Behavioral Science, Queen Mary, University of London, UK
| | - John H Viles
- School of Biological and Behavioral Science, Mile End Road, Queen Mary, University of London, UK, E1 4AS, UK.
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7
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Tian Y, Shang Q, Liang R, Viles JH. Copper(II) Can Kinetically Trap Arctic and Italian Amyloid-β 40 as Toxic Oligomers, Mimicking Cu(II) Binding to Wild-Type Amyloid-β 42: Implications for Familial Alzheimer's Disease. JACS AU 2024; 4:578-591. [PMID: 38425915 PMCID: PMC10900208 DOI: 10.1021/jacsau.3c00687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 03/02/2024]
Abstract
The self-association of amyloid-β (Aβ) peptide into neurotoxic oligomers is believed to be central to Alzheimer's disease (AD). Copper is known to impact Aβ assembly, while disrupted copper homeostasis impacts phenotype in Alzheimer's models. Here we show the presence of substoichiometric Cu(II) has very different impacts on the assembly of Aβ40 and Aβ42 isoforms. Globally fitting microscopic rate constants for fibril assembly indicates copper will accelerate fibril formation of Aβ40 by increasing primary nucleation, while seeding experiments confirm that elongation and secondary nucleation rates are unaffected by Cu(II). In marked contrast, Cu(II) traps Aβ42 as prefibrillar oligomers and curvilinear protofibrils. Remarkably, the Cu(II) addition to preformed Aβ42 fibrils causes the disassembly of fibrils back to protofibrils and oligomers. The very different behaviors of the two Aβ isoforms are centered around differences in their fibril structures, as highlighted by studies of C-terminally amidated Aβ42. Arctic and Italian familiar mutations also support a key role for fibril structure in the interplay of Cu(II) with Aβ40/42 isoforms. The Cu(II) dependent switch in behavior between nonpathogenic Aβ40 wild-type and Aβ40 Arctic or Italian mutants suggests heightened neurotoxicity may be linked to the impact of physiological Cu(II), which traps these familial mutants as oligomers and curvilinear protofibrils, which cause membrane permeability and Ca(II) cellular influx.
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Affiliation(s)
- Yao Tian
- School of Biological and Behavioral
Sciences, Queen Mary University of London, London E1 4NS, U.K.
| | - Qi Shang
- School of Biological and Behavioral
Sciences, Queen Mary University of London, London E1 4NS, U.K.
| | - Ruina Liang
- School of Biological and Behavioral
Sciences, Queen Mary University of London, London E1 4NS, U.K.
| | - John H. Viles
- School of Biological and Behavioral
Sciences, Queen Mary University of London, London E1 4NS, U.K.
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8
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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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9
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Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ, Šarić A. Self-replication of A β42 aggregates occurs on small and isolated fibril sites. Proc Natl Acad Sci U S A 2024; 121:e2220075121. [PMID: 38335256 PMCID: PMC10873593 DOI: 10.1073/pnas.2220075121] [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: 11/24/2022] [Accepted: 11/17/2023] [Indexed: 02/12/2024] Open
Abstract
Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer's A[Formula: see text] amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A[Formula: see text] fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor.
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Affiliation(s)
- Samo Curk
- Institute of Science and Technology Austria, Klosterneuburg3400, Austria
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - Johannes Krausser
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Daan Frenkel
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund22100, Sweden
| | - Thomas C. T. Michaels
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich8093, Switzerland
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Anđela Šarić
- Institute of Science and Technology Austria, Klosterneuburg3400, Austria
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
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10
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Bigi A, Napolitano L, Vadukul DM, Chiti F, Cecchi C, Aprile FA, Cascella R. A single-domain antibody detects and neutralises toxic Aβ 42 oligomers in the Alzheimer's disease CSF. Alzheimers Res Ther 2024; 16:13. [PMID: 38238842 PMCID: PMC10795411 DOI: 10.1186/s13195-023-01361-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/29/2023] [Indexed: 01/22/2024]
Abstract
BACKGROUND Amyloid-β42 (Aβ42) aggregation consists of a complex chain of nucleation events producing soluble oligomeric intermediates, which are considered the major neurotoxic agents in Alzheimer's disease (AD). Cerebral lesions in the brain of AD patients start to develop 20 years before symptom onset; however, no preventive strategies, effective treatments, or specific and sensitive diagnostic tests to identify people with early-stage AD are currently available. In addition, the isolation and characterisation of neurotoxic Aβ42 oligomers are particularly difficult because of their transient and heterogeneous nature. To overcome this challenge, a rationally designed method generated a single-domain antibody (sdAb), named DesAb-O, targeting Aβ42 oligomers. METHODS We investigated the ability of DesAb-O to selectively detect preformed Aβ42 oligomers both in vitro and in cultured neuronal cells, by using dot-blot, ELISA immunoassay and super-resolution STED microscopy, and to counteract the toxicity induced by the oligomers, monitoring their interaction with neuronal membrane and the resulting mitochondrial impairment. We then applied this approach to CSF samples (CSFs) from AD patients as compared to age-matched control subjects. RESULTS DesAb-O was found to selectively detect synthetic Aβ42 oligomers both in vitro and in cultured cells, and to neutralise their associated neuronal dysfunction. DesAb-O can also identify Aβ42 oligomers present in the CSFs of AD patients with respect to healthy individuals, and completely prevent cell dysfunction induced by the administration of CSFs to neuronal cells. CONCLUSIONS Taken together, our data indicate a promising method for the improvement of an early diagnosis of AD and for the generation of novel therapeutic approaches based on sdAbs for the treatment of AD and other devastating neurodegenerative conditions.
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Affiliation(s)
- Alessandra Bigi
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence, Italy
| | - Liliana Napolitano
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence, Italy
| | - Devkee M Vadukul
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence, Italy
| | - Cristina Cecchi
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence, Italy
| | - Francesco A Aprile
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, London, UK
| | - Roberta Cascella
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence, Italy.
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11
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de Raffele D, Ilie IM. Unlocking novel therapies: cyclic peptide design for amyloidogenic targets through synergies of experiments, simulations, and machine learning. Chem Commun (Camb) 2024; 60:632-645. [PMID: 38131333 DOI: 10.1039/d3cc04630c] [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: 12/23/2023]
Abstract
Existing therapies for neurodegenerative diseases like Parkinson's and Alzheimer's address only their symptoms and do not prevent disease onset. Common therapeutic agents, such as small molecules and antibodies struggle with insufficient selectivity, stability and bioavailability, leading to poor performance in clinical trials. Peptide-based therapeutics are emerging as promising candidates, with successful applications for cardiovascular diseases and cancers due to their high bioavailability, good efficacy and specificity. In particular, cyclic peptides have a long in vivo stability, while maintaining a robust antibody-like binding affinity. However, the de novo design of cyclic peptides is challenging due to the lack of long-lived druggable pockets of the target polypeptide, absence of exhaustive conformational distributions of the target and/or the binder, unknown binding site, methodological limitations, associated constraints (failed trials, time, money) and the vast combinatorial sequence space. Hence, efficient alignment and cooperation between disciplines, and synergies between experiments and simulations complemented by popular techniques like machine-learning can significantly speed up the therapeutic cyclic-peptide development for neurodegenerative diseases. We review the latest advancements in cyclic peptide design against amyloidogenic targets from a computational perspective in light of recent advancements and potential of machine learning to optimize the design process. We discuss the difficulties encountered when designing novel peptide-based inhibitors and we propose new strategies incorporating experiments, simulations and machine learning to design cyclic peptides to inhibit the toxic propagation of amyloidogenic polypeptides. Importantly, these strategies extend beyond the mere design of cyclic peptides and serve as template for the de novo generation of (bio)materials with programmable properties.
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Affiliation(s)
- Daria de Raffele
- University of Amsterdam, van 't Hoff Institute for Molecular Sciences, Science Park 904, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands.
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Ioana M Ilie
- University of Amsterdam, van 't Hoff Institute for Molecular Sciences, Science Park 904, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands.
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
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12
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Meyer N, Bentin J, Janot JM, Abrao-Nemeir I, Charles-Achille S, Pratlong M, Aquilina A, Trinquet E, Perrier V, Picaud F, Torrent J, Balme S. Ultrasensitive Detection of Aβ42 Seeds in Cerebrospinal Fluid with a Nanopipette-Based Real-Time Fast Amyloid Seeding and Translocation Assay. Anal Chem 2023; 95:12623-12630. [PMID: 37587130 DOI: 10.1021/acs.analchem.3c00017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
In this work, early-stage Aβ42 aggregates were detected using a real-time fast amyloid seeding and translocation (RT-FAST) assay. Specifically, Aβ42 monomers were incubated in buffer solution with and without preformed Aβ42 seeds in a quartz nanopipette coated with L-DOPA. Then, formed Aβ42 aggregates were analyzed on flyby resistive pulse sensing at various incubation time points. Aβ42 aggregates were detected only in the sample with Aβ42 seeds after 180 min of incubation, giving an on/off readout of the presence of preformed seeds. Moreover, this RT-FAST assay could detect preformed seeds spiked in 4% cerebrospinal fluid/buffer solution. However, in this condition, the time to detect the first aggregates was increased. Analysis of Cy3-labeled Aβ42 monomer adsorption on a quartz substrate after L-DOPA coating by confocal fluorescence spectroscopy and molecular dynamics simulation showed the huge influence of Aβ42 adsorption on the aggregation process.
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Affiliation(s)
- Nathan Meyer
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
- INM UM, CNRS, INSERM, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Jeremy Bentin
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 route de Gray, 25030 Besançon, France
| | - Jean-Marc Janot
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Imad Abrao-Nemeir
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Saly Charles-Achille
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Maud Pratlong
- PerkinElmer, Parc Marcel Boiteux, 30200 Codolet, France
| | | | - Eric Trinquet
- PerkinElmer, Parc Marcel Boiteux, 30200 Codolet, France
| | - Veronique Perrier
- INM UM, CNRS, INSERM, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Fabien Picaud
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 route de Gray, 25030 Besançon, France
| | - Joan Torrent
- INM UM, CNRS, INSERM, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Sebastien Balme
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
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13
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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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14
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Viles JH. Imaging Amyloid-β Membrane Interactions: Ion-Channel Pores and Lipid-Bilayer Permeability in Alzheimer's Disease. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202215785. [PMID: 38515735 PMCID: PMC10952214 DOI: 10.1002/ange.202215785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Indexed: 03/08/2023]
Abstract
The accumulation of the amyloid-β peptides (Aβ) is central to the development of Alzheimer's disease. The mechanism by which Aβ triggers a cascade of events that leads to dementia is a topic of intense investigation. Aβ self-associates into a series of complex assemblies with different structural and biophysical properties. It is the interaction of these oligomeric, protofibril and fibrillar assemblies with lipid membranes, or with membrane receptors, that results in membrane permeability and loss of cellular homeostasis, a key event in Alzheimer's disease pathology. Aβ can have an array of impacts on lipid membranes, reports have included: a carpeting effect; a detergent effect; and Aβ ion-channel pore formation. Recent advances imaging these interactions are providing a clearer picture of Aβ induced membrane disruption. Understanding the relationship between different Aβ structures and membrane permeability will inform therapeutics targeting Aβ cytotoxicity.
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Affiliation(s)
- John H. Viles
- Department of Biochemistry, SBBS, Queen MaryUniversity of LondonUK
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15
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Viles JH. Imaging Amyloid-β Membrane Interactions: Ion-Channel Pores and Lipid-Bilayer Permeability in Alzheimer's Disease. Angew Chem Int Ed Engl 2023; 62:e202215785. [PMID: 36876912 PMCID: PMC10953358 DOI: 10.1002/anie.202215785] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/07/2023]
Abstract
The accumulation of the amyloid-β peptides (Aβ) is central to the development of Alzheimer's disease. The mechanism by which Aβ triggers a cascade of events that leads to dementia is a topic of intense investigation. Aβ self-associates into a series of complex assemblies with different structural and biophysical properties. It is the interaction of these oligomeric, protofibril and fibrillar assemblies with lipid membranes, or with membrane receptors, that results in membrane permeability and loss of cellular homeostasis, a key event in Alzheimer's disease pathology. Aβ can have an array of impacts on lipid membranes, reports have included: a carpeting effect; a detergent effect; and Aβ ion-channel pore formation. Recent advances imaging these interactions are providing a clearer picture of Aβ induced membrane disruption. Understanding the relationship between different Aβ structures and membrane permeability will inform therapeutics targeting Aβ cytotoxicity.
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Affiliation(s)
- John H. Viles
- Department of Biochemistry, SBBS, Queen MaryUniversity of LondonUK
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16
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Wang Y, Xu J, Huang F, Yan J, Fan X, Zou Y, Wang C, Ding F, Sun Y. SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges. J Chem Inf Model 2023; 63:3567-3578. [PMID: 37246935 PMCID: PMC10363411 DOI: 10.1021/acs.jcim.3c00414] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Inhibiting the aggregation of amyloid peptides with endogenous peptides has broad interest due to their intrinsically high biocompatibility and low immunogenicity. Here, we investigated the inhibition mechanism of the prostatic acidic phosphatase fragment SEVI (semen-derived enhancer of viral infection) against Aβ42 fibrillization using atomistic discrete molecular dynamic simulations. Our result revealed that SEVI was intrinsically disordered with dynamic formation of residual helices. With a high positive net charge, the self-aggregation tendency of SEVI was weak. Aβ42 had a strong aggregation propensity by readily self-assembling into β-sheet-rich aggregates. SEVI preferred to interact with Aβ42, rather than SEVI themselves. In the heteroaggregates, Aβ42 mainly adopted β-sheets buried inside and capped by SEVI in the outer layer. SEVI could bind to various Aβ aggregation species─including monomers, dimers, and proto-fibrils─by capping the exposed β-sheet elongation edges. The aggregation processes Aβ42 from the formation of oligomers to conformational nucleation into fibrils and fibril growth should be inhibited as their β-sheet elongation edges are being occupied by the highly charged SEVI. Overall, our computational study uncovered the molecular mechanism of experimentally observed inhibition of SEVI against Aβ42 aggregation, providing novel insights into the development of therapeutic strategies against Alzheimer's disease.
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Affiliation(s)
- Ying Wang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, China
| | - Jia Xu
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Fengjuan Huang
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, China
| | - Jiajia Yan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Xinjie Fan
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yu Zou
- Department of Sport and Exercise Science, Zhejiang University, Hangzhou 310058, China
| | - Chuang Wang
- School of Medicine, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Ningbo Institute of Innovation for Combined Medicine and Engineering (NIIME), Ningbo Medical Center Lihuili Hospital, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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17
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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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18
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Ghosh S, Ali R, Verma S. Aβ-oligomers: A potential therapeutic target for Alzheimer's disease. Int J Biol Macromol 2023; 239:124231. [PMID: 36996958 DOI: 10.1016/j.ijbiomac.2023.124231] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/22/2023] [Accepted: 03/25/2023] [Indexed: 03/30/2023]
Abstract
The cascade of amyloid formation relates to multiple complex events at the molecular level. Previous research has established amyloid plaque deposition as the leading cause of Alzheimer's disease (AD) pathogenesis, detected mainly in aged population. The primary components of the plaques are two alloforms of amyloid-beta (Aβ), Aβ1-42 and Aβ1-40 peptides. Recent studies have provided considerable evidence contrary to the previous claim indicating that amyloid-beta oligomers (AβOs) as the main culprit responsible for AD-associated neurotoxicity and pathogenesis. In this review, we have discussed the primary features of AβOs, such as assembly formation, the kinetics of oligomer formation, interactions with various membranes/membrane receptors, the origin of toxicity, and oligomer-specific detection methods. Recently, the discovery of rationally designed antibodies has opened a gateway for using synthesized peptides as a grafting component in the complementarity determining region (CDR) of antibodies. Thus, the Aβ sequence motif or the complementary peptide sequence in the opposite strand of the β-sheet (extracted from the Protein Data Bank: PDB) helps design oligomer-specific inhibitors. The microscopic event responsible for oligomer formation can be targeted, and thus prevention of the overall macroscopic behaviour of the aggregation or the associated toxicity can be achieved. We have carefully reviewed the oligomer formation kinetics and associated parameters. Besides, we have depicted a thorough understanding of how the synthesized peptide inhibitors can impede the early aggregates (oligomers), mature fibrils, monomers, or a mixture of the species. The oligomer-specific inhibitors (peptides or peptide fragments) lack in-depth chemical kinetics and optimization control-based screening. In the present review, we have proposed a hypothesis for effectively screening oligomer-specific inhibitors using the chemical kinetics (determining the kinetic parameters) and optimization control strategy (cost-dependent analysis). Further, it may be possible to implement the structure-kinetic-activity-relationship (SKAR) strategy instead of structure-activity-relationship (SAR) to improve the inhibitor's activity. The controlled optimization of the kinetic parameters and dose usage will be beneficial for narrowing the search window for the inhibitors.
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19
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Khalifa J, Bourgault S, Gaudreault R. Interactions of Polyphenolic Gallotannins with Amyloidogenic Polypeptides Associated with Alzheimer's Disease: From Molecular Insights to Physiological Significance. Curr Alzheimer Res 2023; 20:603-617. [PMID: 38270140 DOI: 10.2174/0115672050277001231213073043] [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: 08/31/2023] [Revised: 10/30/2023] [Accepted: 11/10/2023] [Indexed: 01/26/2024]
Abstract
Polyphenols are natural compounds abundantly found in plants. They are known for their numerous benefits to human health, including antioxidant properties and anti-inflammatory activities. Interestingly, many studies have revealed that polyphenols can also modulate the formation of amyloid fibrils associated with disease states and can prevent the formation of cytotoxic oligomer species. In this review, we underline the numerous effects of four hydrolysable gallotannins (HGTs) with high conformational flexibility, low toxicity, and multi-targeticity, e.g., tannic acid, pentagalloyl glucose, corilagin, and 1,3,6-tri-O-galloyl-β-D-glucose, on the aggregation of amyloidogenic proteins associated with the Alzheimer's Disease (AD). These HGTs have demonstrated interesting abilities to reduce, at different levels, the formation of amyloid fibrils involved in AD, including those assembled from the amyloid β-peptide, the tubulin-associated unit, and the islet amyloid polypeptide. HGTs were also shown to disassemble pre-formed fibrils and to diminish cognitive decline in mice. Finally, this manuscript highlights the importance of further investigating these naturally occurring HGTs as promising scaffolds to design molecules that can interfere with the formation of proteotoxic oligomers and aggregates associated with AD pathogenesis.
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Affiliation(s)
- Jihane Khalifa
- Département de Chimie, Université du Québec à Montréal, 2101 Rue Jeanne-Mance, Montréal, QC, H2X 2J6, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Canada
- Quebec Centre for Advanced Materials (QCAM), 3420 University Street, Montréal, QC, H2X 3Y7, Canada
| | - Steve Bourgault
- Département de Chimie, Université du Québec à Montréal, 2101 Rue Jeanne-Mance, Montréal, QC, H2X 2J6, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Canada
| | - Roger Gaudreault
- Département de Chimie, Université du Québec à Montréal, 2101 Rue Jeanne-Mance, Montréal, QC, H2X 2J6, Canada
- Quebec Centre for Advanced Materials (QCAM), 3420 University Street, Montréal, QC, H2X 3Y7, Canada
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20
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Kulenkampff K, Emin D, Staats R, Zhang YP, Sakhnini L, Kouli A, Rimon O, Lobanova E, Williams-Gray CH, Aprile FA, Sormanni P, Klenerman D, Vendruscolo M. An antibody scanning method for the detection of α-synuclein oligomers in the serum of Parkinson's disease patients. Chem Sci 2022; 13:13815-13828. [PMID: 36544716 PMCID: PMC9710209 DOI: 10.1039/d2sc00066k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 09/16/2022] [Indexed: 01/16/2023] Open
Abstract
Misfolded α-synuclein oligomers are closely implicated in the pathology of Parkinson's disease and related synucleinopathies. The elusive nature of these aberrant assemblies makes it challenging to develop quantitative methods to detect them and modify their behavior. Existing detection methods use antibodies to bind α-synuclein aggregates in biofluids, although it remains challenging to raise antibodies against α-synuclein oligomers. To address this problem, we used an antibody scanning approach in which we designed a panel of 9 single-domain epitope-specific antibodies against α-synuclein. We screened these antibodies for their ability to inhibit the aggregation process of α-synuclein, finding that they affected the generation of α-synuclein oligomers to different extents. We then used these antibodies to investigate the size distribution and morphology of soluble α-synuclein aggregates in serum and cerebrospinal fluid samples from Parkinson's disease patients. Our results indicate that the approach that we present offers a promising route for the development of antibodies to characterize soluble α-synuclein aggregates in biofluids.
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Affiliation(s)
- Klara Kulenkampff
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of CambridgeCambridge CB2 1EWUK
| | - Derya Emin
- Yusuf Hamied Department of Chemistry, University of CambridgeCambridgeCB2 1EWUK,UK Dementia Research Institute, University of CambridgeCambridgeCB2 0XYUK
| | - Roxine Staats
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of CambridgeCambridge CB2 1EWUK
| | - Yu P. Zhang
- Yusuf Hamied Department of Chemistry, University of CambridgeCambridgeCB2 1EWUK
| | - Laila Sakhnini
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of CambridgeCambridge CB2 1EWUK
| | - Antonina Kouli
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of CambridgeUK
| | - Oded Rimon
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of CambridgeCambridge CB2 1EWUK
| | - Evgeniia Lobanova
- Yusuf Hamied Department of Chemistry, University of CambridgeCambridgeCB2 1EWUK,UK Dementia Research Institute, University of CambridgeCambridgeCB2 0XYUK
| | - Caroline H. Williams-Gray
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of CambridgeUK
| | - Francesco A. Aprile
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of CambridgeCambridge CB2 1EWUK
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of CambridgeCambridge CB2 1EWUK
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of CambridgeCambridgeCB2 1EWUK,UK Dementia Research Institute, University of CambridgeCambridgeCB2 0XYUK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of CambridgeCambridge CB2 1EWUK
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21
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Tian Y, Viles JH. pH Dependence of Amyloid-β Fibril Assembly Kinetics: Unravelling the Microscopic Molecular Processes. Angew Chem Int Ed Engl 2022; 61:e202210675. [PMID: 36197009 PMCID: PMC9828734 DOI: 10.1002/anie.202210675] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Indexed: 11/05/2022]
Abstract
Central to Alzheimer's disease (AD) is the assembly of the amyloid-beta peptide (Aβ) into fibrils. A reduction in pH accompanying inflammation or subcellular compartments, may accelerate fibril formation as the pH approaches Aβ's isoelectric point (pI). Using global fitting of fibril formation kinetics over a range of pHs, we identify the impact net charge has on individual fibril assembly microscopic rate constants. We show that the primary nucleation has a strong pH dependence. The titration behaviour exhibits a mid-point or pKa of 7.0, close to the pKa of Aβ histidine imidazoles. Surprisingly, both the secondary nucleation and elongation rate constants are pH independent. This indicates the charge of Aβ, in particular histidine protonation, has little impact on this stage of Aβ assembly. These fundamental processes are key to understanding the forces that drive the assembly of Aβ into toxic oligomers and fibrils.
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Affiliation(s)
- Yao Tian
- Department of BiochemistrySchool of Biological and Behavioural SciencesQueen Mary University of LondonLondonUK
| | - John H. Viles
- Department of BiochemistrySchool of Biological and Behavioural SciencesQueen Mary University of LondonLondonUK
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22
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Tian Y, Viles JH. pH Dependence of Amyloid-β Fibril Assembly Kinetics: Unravelling the Microscopic Molecular Processes. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202210675. [PMID: 38504922 PMCID: PMC10947324 DOI: 10.1002/ange.202210675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Indexed: 11/09/2022]
Abstract
Central to Alzheimer's disease (AD) is the assembly of the amyloid-beta peptide (Aβ) into fibrils. A reduction in pH accompanying inflammation or subcellular compartments, may accelerate fibril formation as the pH approaches Aβ's isoelectric point (pI). Using global fitting of fibril formation kinetics over a range of pHs, we identify the impact net charge has on individual fibril assembly microscopic rate constants. We show that the primary nucleation has a strong pH dependence. The titration behaviour exhibits a mid-point or pK a of 7.0, close to the pK a of Aβ histidine imidazoles. Surprisingly, both the secondary nucleation and elongation rate constants are pH independent. This indicates the charge of Aβ, in particular histidine protonation, has little impact on this stage of Aβ assembly. These fundamental processes are key to understanding the forces that drive the assembly of Aβ into toxic oligomers and fibrils.
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Affiliation(s)
- Yao Tian
- Department of BiochemistrySchool of Biological and Behavioural SciencesQueen Mary University of LondonLondonUK
| | - John H. Viles
- Department of BiochemistrySchool of Biological and Behavioural SciencesQueen Mary University of LondonLondonUK
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23
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Aguilar Rangel M, Bedwell A, Costanzi E, Taylor RJ, Russo R, Bernardes GJL, Ricagno S, Frydman J, Vendruscolo M, Sormanni P. Fragment-based computational design of antibodies targeting structured epitopes. SCIENCE ADVANCES 2022; 8:eabp9540. [PMID: 36367941 PMCID: PMC9651861 DOI: 10.1126/sciadv.abp9540] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
De novo design methods hold the promise of reducing the time and cost of antibody discovery while enabling the facile and precise targeting of predetermined epitopes. Here, we describe a fragment-based method for the combinatorial design of antibody binding loops and their grafting onto antibody scaffolds. We designed and tested six single-domain antibodies targeting different epitopes on three antigens, including the receptor-binding domain of the SARS-CoV-2 spike protein. Biophysical characterization showed that all designs are stable and bind their intended targets with affinities in the nanomolar range without in vitro affinity maturation. We further discuss how a high-resolution input antigen structure is not required, as similar predictions are obtained when the input is a crystal structure or a computer-generated model. This computational procedure, which readily runs on a laptop, provides a starting point for the rapid generation of lead antibodies binding to preselected epitopes.
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Affiliation(s)
- Mauricio Aguilar Rangel
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Alice Bedwell
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Elisa Costanzi
- Department of Bioscience, Università degli Studi di Milano, Milano 20133, Italy
| | - Ross J. Taylor
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Rosaria Russo
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milano 20122, Italy
| | - Gonçalo J. L. Bernardes
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Stefano Ricagno
- Department of Bioscience, Università degli Studi di Milano, Milano 20133, Italy
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Milan 20097, Italy
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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24
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Tian Y, Liu J, Yang F, Lian C, Zhang H, Viles JH, Li Z. Therapeutic potential for amyloid surface inhibitor: only amyloid-β oligomers formed by secondary nucleation disrupt lipid membrane integrity. FEBS J 2022; 289:6767-6781. [PMID: 35670622 DOI: 10.1111/febs.16550] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/11/2022] [Accepted: 06/06/2022] [Indexed: 01/01/2023]
Abstract
Inhibition of amyloid-β peptide (Aβ) aggregation is a promising therapeutic strategy for Alzheimer's disease (AD), as Aβ aggregation is generally believed to trigger AD pathology. Pre-fibril Aβ-oligomers induce membrane disruption and are crucial to neurotoxicity. We have previously designed a short peptide called cyclic helical amyloid surface inhibitor (cHASI) that can selectively bind to the Aβ fibril surface. Here, we use cHASI to efficiently inhibit the surface-catalysed secondary nucleation process of Aβ in a lipid membrane environment. By incubating Aβ monomers with lipid vesicles, we show that during the assembly of Aβ into amyloid fibrils, oligomers are formed that markedly disrupt the lipid bilayer. Remarkably, when Aβ monomers are incubated with cHASI, although Aβ forms amyloid fibrils via primary nucleation and elongation, this pathway to fibrils does not damage the lipid bilayer. This indicates that only oligomers produced during secondary surface nucleation disrupt membrane integrity. The protective effect of cHASI is confirmed by cytotoxicity assays. Our study highlights the therapeutic potential for inhibiting the secondary nucleation process in Aβ aggregation, rather than inhibiting all pathways to fibril formation.
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Affiliation(s)
- Yao Tian
- School of Biological and Chemical Sciences, Queen Mary University of London, UK
| | - Jianbo Liu
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, China
| | - Fadeng Yang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, China
| | - Chenshan Lian
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, China
| | - Huawei Zhang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - John H Viles
- School of Biological and Chemical Sciences, Queen Mary University of London, UK
| | - Zigang Li
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, China.,State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, China
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25
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Wong MTY, Kelm S, Liu X, Taylor RD, Baker T, Essex JW. Higher Affinity Antibodies Bind With Lower Hydration and Flexibility in Large Scale Simulations. Front Immunol 2022; 13:884110. [PMID: 35707541 PMCID: PMC9190259 DOI: 10.3389/fimmu.2022.884110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/22/2022] [Indexed: 11/25/2022] Open
Abstract
We have carried out a long-timescale simulation study on crystal structures of nine antibody-antigen pairs, in antigen-bound and antibody-only forms, using molecular dynamics with enhanced sampling and an explicit water model to explore interface conformation and hydration. By combining atomic level simulation and replica exchange to enable full protein flexibility, we find significant numbers of bridging water molecules at the antibody-antigen interface. Additionally, a higher proportion of interactions excluding bulk waters and a lower degree of antigen bound CDR conformational sampling are correlated with higher antibody affinity. The CDR sampling supports enthalpically driven antibody binding, as opposed to entropically driven, in that the difference between antigen bound and unbound conformations do not correlate with affinity. We thus propose that interactions with waters and CDR sampling are aspects of the interface that may moderate antibody-antigen binding, and that explicit hydration and CDR flexibility should be considered to improve antibody affinity prediction and computational design workflows.
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Affiliation(s)
- Mabel T. Y. Wong
- School of Chemistry, University of Southampton, Southampton, United Kingdom
| | | | | | | | | | - Jonathan W. Essex
- School of Chemistry, University of Southampton, Southampton, United Kingdom
- *Correspondence: Jonathan W. Essex,
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26
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An aggregation inhibitor specific to oligomeric intermediates of Aβ42 derived from phage display libraries of stable, small proteins. Proc Natl Acad Sci U S A 2022; 119:e2121966119. [PMID: 35580187 PMCID: PMC9173773 DOI: 10.1073/pnas.2121966119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Alzheimer’s disease affects a growing number of people, but a cure is lacking. The disease is connected to the formation of plaques in the brain, the first of which appear years before the first symptoms. Current approaches fail to stop or revert the propagation of these plaques, which are also a source of neurotoxic species in the form of oligomers. This work represents two directions toward therapeutic developments: 1) the design and production of protein libraries based on a small and stable scaffold, and 2) the realization of a screening procedure that allows for the identification of oligomer binders. The approach is successful in identifying a candidate protein that binds to oligomers and reduces the rate of plaque proliferation. The self-assembly of amyloid β peptide (Aβ) to fibrillar and oligomeric aggregates is linked to Alzheimer’s disease. Aβ binders may serve as inhibitors of aggregation to prevent the generation of neurotoxic species and for the detection of Aβ species. A particular challenge involves finding binders to on-pathway oligomers given their transient nature. Here we construct two phage–display libraries built on the highly inert and stable protein scaffold S100G, one containing a six-residue variable surface patch and one harboring a seven-residue variable loop insertion. Monomers and fibrils of Aβ40 and Aβ42 were separately coupled to silica nanoparticles, using a coupling strategy leading to the presence of oligomers on the monomer beads, and they were used in three rounds of affinity selection. Next-generation sequencing revealed sequence clusters and candidate binding proteins (SXkmers). Two SXkmers were expressed as soluble proteins and tested in terms of aggregation inhibition via thioflavin T fluorescence. We identified an SXkmer with loop–insertion YLTIRLM as an inhibitor of the secondary nucleation of Aβ42 and binding analyses using surface plasmon resonance technology, Förster resonance energy transfer, and microfluidics diffusional sizing imply an interaction with intermediate oligomeric species. A linear peptide with the YLTIRLM sequence was found inhibitory but at a lower potency than the more constrained SXkmer loop. We identified an SXkmer with side-patch VI-WI-DD as an inhibitor of Aβ40 aggregation. Remarkably, our data imply that SXkmer-YLTIRLM blocks secondary nucleation through an interaction with oligomeric intermediates in solution or at the fibril surface, which is a unique inhibitory mechanism for a library-derived inhibitor.
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27
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Löhr T, Sormanni P, Vendruscolo M. Conformational Entropy as a Potential Liability of Computationally Designed Antibodies. Biomolecules 2022; 12:718. [PMID: 35625644 PMCID: PMC9138470 DOI: 10.3390/biom12050718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/06/2022] [Accepted: 05/08/2022] [Indexed: 01/28/2023] Open
Abstract
In silico antibody discovery is emerging as a viable alternative to traditional in vivo and in vitro approaches. Many challenges, however, remain open to enabling the properties of designed antibodies to match those produced by the immune system. A major question concerns the structural features of computer-designed complementarity determining regions (CDRs), including the role of conformational entropy in determining the stability and binding affinity of the designed antibodies. To address this problem, we used enhanced-sampling molecular dynamics simulations to compare the free energy landscapes of single-domain antibodies (sdAbs) designed using structure-based (DesAb-HSA-D3) and sequence-based approaches (DesAbO), with that of a nanobody derived from llama immunization (Nb10). Our results indicate that the CDR3 of DesAbO is more conformationally heterogeneous than those of both DesAb-HSA-D3 and Nb10, and the CDR3 of DesAb-HSA-D3 is slightly more dynamic than that of Nb10, which is the original scaffold used for the design of DesAb-HSA-D3. These differences underline the challenges in the rational design of antibodies by revealing the presence of conformational substates likely to have different binding properties and to generate a high entropic cost upon binding.
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Affiliation(s)
| | | | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK; (T.L.); (P.S.)
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28
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Modeling Alzheimer's Disease in Caenorhabditis elegans. Biomedicines 2022; 10:biomedicines10020288. [PMID: 35203497 PMCID: PMC8869312 DOI: 10.3390/biomedicines10020288] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Alzheimer’s disease (AD) is the most frequent cause of dementia. After decades of research, we know the importance of the accumulation of protein aggregates such as β-amyloid peptide and phosphorylated tau. We also know that mutations in certain proteins generate early-onset Alzheimer’s disease (EOAD), and many other genes modulate the disease in its sporadic form. However, the precise molecular mechanisms underlying AD pathology are still unclear. Because of ethical limitations, we need to use animal models to investigate these processes. The nematode Caenorhabditis elegans has received considerable attention in the last 25 years, since the first AD models overexpressing Aβ peptide were described. We review here the main results obtained using this model to study AD. We include works studying the basic molecular mechanisms of the disease, as well as those searching for new therapeutic targets. Although this model also has important limitations, the ability of this nematode to generate knock-out or overexpression models of any gene, single or combined, and to carry out toxicity, recovery or survival studies in short timeframes with many individuals and at low cost is difficult to overcome. We can predict that its use as a model for various diseases will certainly continue to increase.
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29
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Pras A, Houben B, Aprile FA, Seinstra R, Gallardo R, Janssen L, Hogewerf W, Gallrein C, De Vleeschouwer M, Mata‐Cabana A, Koopman M, Stroo E, de Vries M, Louise Edwards S, Kirstein J, Vendruscolo M, Falsone SF, Rousseau F, Schymkowitz J, Nollen EAA. The cellular modifier MOAG-4/SERF drives amyloid formation through charge complementation. EMBO J 2021; 40:e107568. [PMID: 34617299 PMCID: PMC8561633 DOI: 10.15252/embj.2020107568] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 08/27/2021] [Accepted: 09/01/2021] [Indexed: 11/09/2022] Open
Abstract
While aggregation-prone proteins are known to accelerate aging and cause age-related diseases, the cellular mechanisms that drive their cytotoxicity remain unresolved. The orthologous proteins MOAG-4, SERF1A, and SERF2 have recently been identified as cellular modifiers of such proteotoxicity. Using a peptide array screening approach on human amyloidogenic proteins, we found that SERF2 interacted with protein segments enriched in negatively charged and hydrophobic, aromatic amino acids. The absence of such segments, or the neutralization of the positive charge in SERF2, prevented these interactions and abolished the amyloid-promoting activity of SERF2. In protein aggregation models in the nematode worm Caenorhabditis elegans, protein aggregation and toxicity were suppressed by mutating the endogenous locus of MOAG-4 to neutralize charge. Our data indicate that MOAG-4 and SERF2 drive protein aggregation and toxicity by interactions with negatively charged segments in aggregation-prone proteins. Such charge interactions might accelerate primary nucleation of amyloid by initiating structural changes and by decreasing colloidal stability. Our study points at charge interactions between cellular modifiers and amyloidogenic proteins as potential targets for interventions to reduce age-related protein toxicity.
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Affiliation(s)
- Anita Pras
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Bert Houben
- VIB‐KU Leuven Center for Brain and Disease ResearchLeuvenBelgium
- Switch LaboratoryDepartment of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Francesco A Aprile
- Department of ChemistryCentre for Misfolding DiseasesUniversity of CambridgeCambridgeUK
- Present address:
Department of ChemistryMolecular Sciences Research HubImperial College LondonLondonUK
| | - Renée Seinstra
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Rodrigo Gallardo
- VIB‐KU Leuven Center for Brain and Disease ResearchLeuvenBelgium
- Switch LaboratoryDepartment of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
- Present address:
Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
| | - Leen Janssen
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Wytse Hogewerf
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Christian Gallrein
- Department of Molecular Physiology and Cell BiologyLeibniz Research Institute for Molecular Pharmacology im Forschungsverbund Berlin e.V. (FMP)BerlinGermany
| | - Matthias De Vleeschouwer
- VIB‐KU Leuven Center for Brain and Disease ResearchLeuvenBelgium
- Switch LaboratoryDepartment of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Alejandro Mata‐Cabana
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Mandy Koopman
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Esther Stroo
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Minke de Vries
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Samantha Louise Edwards
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Janine Kirstein
- Department of Molecular Physiology and Cell BiologyLeibniz Research Institute for Molecular Pharmacology im Forschungsverbund Berlin e.V. (FMP)BerlinGermany
- Faculty of Biology & ChemistryUniversity of BremenBremenGermany
| | - Michele Vendruscolo
- Department of ChemistryCentre for Misfolding DiseasesUniversity of CambridgeCambridgeUK
| | | | - Frederic Rousseau
- VIB‐KU Leuven Center for Brain and Disease ResearchLeuvenBelgium
- Switch LaboratoryDepartment of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Joost Schymkowitz
- VIB‐KU Leuven Center for Brain and Disease ResearchLeuvenBelgium
- Switch LaboratoryDepartment of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Ellen A A Nollen
- European Research Institute for the Biology of AgeingUniversity of GroningenUniversity Medical Centre GroningenGroningenThe Netherlands
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30
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Lin J, Figazzolo C, Metrick MA, Sormanni P, Vendruscolo M. Computational maturation of a single-domain antibody against Aβ42 aggregation. Chem Sci 2021; 12:13940-13948. [PMID: 35475123 PMCID: PMC8901120 DOI: 10.1039/d1sc03898b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/23/2021] [Indexed: 02/02/2023] Open
Abstract
The expansion of structural databases and the increase in computing power are enabling approaches for antibody discovery based on computational design. It has already been shown that it is possible to use this approach to generate antibodies for specific epitopes on challenging targets. Here we describe an application of this procedure for antibody maturation through the computational design of mutational variants of increased potency. We illustrate this procedure in the case of a single-domain antibody targeting an epitope in the N-terminal region of Aβ42, a peptide whose aggregation is closely associated with Alzheimer's disease. We show that this approach enables the generation of an antibody variant with over 200-fold increased potency against the primary nucleation process in Aβ42 aggregation. Our results thus demonstrate that potentiated antibody variants can be obtained by computational maturation. A computational maturation method enables the generation of an antibody variant with over 200-fold increased potency against the primary nucleation process in Aβ42 aggregation.![]()
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Affiliation(s)
- Jiacheng Lin
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Chiara Figazzolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Michael A Metrick
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
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31
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Sharma S, Modi P, Sharma G, Deep S. Kinetics theories to understand the mechanism of aggregation of a protein and to design strategies for its inhibition. Biophys Chem 2021; 278:106665. [PMID: 34419715 DOI: 10.1016/j.bpc.2021.106665] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022]
Abstract
Protein aggregation phenomenon is closely related to the formation of amyloids which results in many neurodegenerative diseases like Alzheimer's, Parkinson's, Huntington's, and Amyotrophic Lateral Sclerosis. In order to prevent and treat these diseases, a clear understanding of the mechanism of misfolding and self-assembly of peptides and proteins is very crucial. The aggregation of a protein may involve various microscopic events. Multiple simulations utilizing the solutions of the master equation have given a better understanding of the kinetic profiles involved in the presence and absence of a particular microscopic event. This review focuses on understanding the contribution of these molecular events to protein aggregation based on the analysis of kinetic profiles of aggregation. We also discuss the effect of inhibitors, which target various species of aggregation pathways, on the kinetic profile of protein aggregation. At the end of this review, some strategies for the inhibition of aggregation that can be utilized by combining the chemical kinetics approach with thermodynamics are proposed.
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Affiliation(s)
- Shilpa Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Priya Modi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Gargi Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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32
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Dear AJ, Michaels TCT, Knowles TPJ, Mahadevan L. Feedback control of protein aggregation. J Chem Phys 2021; 155:064102. [PMID: 34391352 DOI: 10.1063/5.0055925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The self-assembly of peptides and proteins into amyloid fibrils plays a causative role in a wide range of increasingly common and currently incurable diseases. The molecular mechanisms underlying this process have recently been discovered, prompting the development of drugs that inhibit specific reaction steps as possible treatments for some of these disorders. A crucial part of treatment design is to determine how much drug to give and when to give it, informed by its efficacy and intrinsic toxicity. Since amyloid formation does not proceed at the same pace in different individuals, it is also important that treatment design is informed by local measurements of the extent of protein aggregation. Here, we use stochastic optimal control theory to determine treatment regimens for inhibitory drugs targeting several key reaction steps in protein aggregation, explicitly taking into account variability in the reaction kinetics. We demonstrate how these regimens may be updated "on the fly" as new measurements of the protein aggregate concentration become available, in principle, enabling treatments to be tailored to the individual. We find that treatment timing, duration, and drug dosage all depend strongly on the particular reaction step being targeted. Moreover, for some kinds of inhibitory drugs, the optimal regimen exhibits high sensitivity to stochastic fluctuations. Feedback controls tailored to the individual may therefore substantially increase the effectiveness of future treatments.
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Affiliation(s)
- Alexander J Dear
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Thomas C T Michaels
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - L Mahadevan
- School of Engineering and Applied Sciences, Department of Physics, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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33
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Rice LJ, Ecroyd H, van Oijen AM. Illuminating amyloid fibrils: Fluorescence-based single-molecule approaches. Comput Struct Biotechnol J 2021; 19:4711-4724. [PMID: 34504664 PMCID: PMC8405898 DOI: 10.1016/j.csbj.2021.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/15/2022] Open
Abstract
The aggregation of proteins into insoluble filamentous amyloid fibrils is a pathological hallmark of neurodegenerative diseases that include Parkinson's disease and Alzheimer's disease. Since the identification of amyloid fibrils and their association with disease, there has been much work to describe the process by which fibrils form and interact with other proteins. However, due to the dynamic nature of fibril formation and the transient and heterogeneous nature of the intermediates produced, it can be challenging to examine these processes using techniques that rely on traditional ensemble-based measurements. Single-molecule approaches overcome these limitations as rare and short-lived species within a population can be individually studied. Fluorescence-based single-molecule methods have proven to be particularly useful for the study of amyloid fibril formation. In this review, we discuss the use of different experimental single-molecule fluorescence microscopy approaches to study amyloid fibrils and their interaction with other proteins, in particular molecular chaperones. We highlight the mechanistic insights these single-molecule techniques have already provided in our understanding of how fibrils form, and comment on their potential future use in studying amyloid fibrils and their intermediates.
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Affiliation(s)
- Lauren J. Rice
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Heath Ecroyd
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Antoine M. van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
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34
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Perni M, Mannini B, Xu CK, Kumita JR, Dobson CM, Chiti F, Vendruscolo M. Exogenous misfolded protein oligomers can cross the intestinal barrier and cause a disease phenotype in C. elegans. Sci Rep 2021; 11:14391. [PMID: 34257326 PMCID: PMC8277765 DOI: 10.1038/s41598-021-93527-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
Misfolded protein oligomers are increasingly recognized as highly cytotoxic agents in a wide range of human disorders associated with protein aggregation. In this study, we assessed the possible uptake and resulting toxic effects of model protein oligomers administered to C. elegans through the culture medium. We used an automated machine-vision, high-throughput screening procedure to monitor the phenotypic changes in the worms, in combination with confocal microscopy to monitor the diffusion of the oligomers, and oxidative stress assays to detect their toxic effects. Our results suggest that the oligomers can diffuse from the intestinal lumen to other tissues, resulting in a disease phenotype. We also observed that pre-incubation of the oligomers with a molecular chaperone (αB-crystallin) or a small molecule inhibitor of protein aggregation (squalamine), reduced the oligomer absorption. These results indicate that exogenous misfolded protein oligomers can be taken up by the worms from their environment and spread across tissues, giving rise to pathological effects in regions distant from their place of absorbance.
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Affiliation(s)
- Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Benedetta Mannini
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Catherine K Xu
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Janet R Kumita
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy.
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
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35
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Limbocker R, Staats R, Chia S, Ruggeri FS, Mannini B, Xu CK, Perni M, Cascella R, Bigi A, Sasser LR, Block NR, Wright AK, Kreiser RP, Custy ET, Meisl G, Errico S, Habchi J, Flagmeier P, Kartanas T, Hollows JE, Nguyen LT, LeForte K, Barbut D, Kumita JR, Cecchi C, Zasloff M, Knowles TPJ, Dobson CM, Chiti F, Vendruscolo M. Squalamine and Its Derivatives Modulate the Aggregation of Amyloid-β and α-Synuclein and Suppress the Toxicity of Their Oligomers. Front Neurosci 2021; 15:680026. [PMID: 34220435 PMCID: PMC8249941 DOI: 10.3389/fnins.2021.680026] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/16/2021] [Indexed: 12/14/2022] Open
Abstract
The aberrant aggregation of proteins is a key molecular event in the development and progression of a wide range of neurodegenerative disorders. We have shown previously that squalamine and trodusquemine, two natural products in the aminosterol class, can modulate the aggregation of the amyloid-β peptide (Aβ) and of α-synuclein (αS), which are associated with Alzheimer's and Parkinson's diseases. In this work, we expand our previous analyses to two squalamine derivatives, des-squalamine and α-squalamine, obtaining further insights into the mechanism by which aminosterols modulate Aβ and αS aggregation. We then characterize the ability of these small molecules to alter the physicochemical properties of stabilized oligomeric species in vitro and to suppress the toxicity of these aggregates to varying degrees toward human neuroblastoma cells. We found that, despite the fact that these aminosterols exert opposing effects on Aβ and αS aggregation under the conditions that we tested, the modifications that they induced to the toxicity of oligomers were similar. Our results indicate that the suppression of toxicity is mediated by the displacement of toxic oligomeric species from cellular membranes by the aminosterols. This study, thus, provides evidence that aminosterols could be rationally optimized in drug discovery programs to target oligomer toxicity in Alzheimer's and Parkinson's diseases.
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Affiliation(s)
- Ryan Limbocker
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Chemistry & Life Science, United States Military Academy, West Point, NY, United States
| | - Roxine Staats
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Sean Chia
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Francesco S. Ruggeri
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Laboratory of Organic Chemistry, Wageningen University, Wageningen, Netherlands
- Laboratory of Physical Chemistry, Wageningen University, Wageningen, Netherlands
| | - Benedetta Mannini
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Catherine K. Xu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Michele Perni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Roberta Cascella
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Alessandra Bigi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Liam R. Sasser
- Department of Chemistry & Life Science, United States Military Academy, West Point, NY, United States
| | - Natalie R. Block
- Department of Chemistry & Life Science, United States Military Academy, West Point, NY, United States
| | - Aidan K. Wright
- Department of Chemistry & Life Science, United States Military Academy, West Point, NY, United States
| | - Ryan P. Kreiser
- Department of Chemistry & Life Science, United States Military Academy, West Point, NY, United States
| | - Edward T. Custy
- Department of Chemistry & Life Science, United States Military Academy, West Point, NY, United States
| | - Georg Meisl
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Silvia Errico
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Johnny Habchi
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Patrick Flagmeier
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tadas Kartanas
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jared E. Hollows
- Department of Chemistry & Life Science, United States Military Academy, West Point, NY, United States
| | - Lam T. Nguyen
- Department of Chemistry & Life Science, United States Military Academy, West Point, NY, United States
| | - Kathleen LeForte
- Department of Chemistry & Life Science, United States Military Academy, West Point, NY, United States
| | | | - Janet R. Kumita
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Cristina Cecchi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Michael Zasloff
- Enterin Inc., Philadelphia, PA, United States
- MedStar Georgetown Transplant Institute, School of Medicine, Georgetown University, Washington, DC, United States
| | - Tuomas P. J. Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Christopher M. Dobson
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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36
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Li G, Zhou Y, Yang WY, Zhang C, Hong L, Jia L. Inhibitory Effects of Sulfated Polysaccharides from the Sea Cucumber Cucumaria Frondosa against Aβ40 Aggregation and Cytotoxicity. ACS Chem Neurosci 2021; 12:1854-1859. [PMID: 33999600 DOI: 10.1021/acschemneuro.1c00223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Abnormal aggregation and deposition of Aβ is one of the causative agents for Alzheimer's disease. The development of inhibitors for Aβ aggregation has been considered a possible method to prevent and treat Alzheimer's disease. Edible sea cucumbers contain many bioactive molecules, including saponins, phospholipids, peptides, and polysaccharides. Herein, we report that polysaccharides extracted from sea cucumber Cucumaria frondosa could reduce the aggregation and cytotoxicity of Aβ40. By utilizing multiple biochemical and biophysical instruments, we found that the polysaccharides could inhibit the aggregation of Aβ40. A chemical kinetics analysis further suggested that the major inhibitory effects of the polysaccharides were achieved by disassembling mature fibrils, which in turn reduced the cytotoxicity of Aβ. These results suggested that the polysaccharides extracted from sea cucumber could be used as an effective inhibitor for Aβ.
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Affiliation(s)
- Gao Li
- Institute of Oceanography, Minjiang University, Fuzhou, Fujian 350108, China
| | - Yu Zhou
- Institute of Oceanography, Minjiang University, Fuzhou, Fujian 350108, China
| | - Wu-Yue Yang
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, Beijing 100084, China
| | - Chen Zhang
- Institute of Oceanography, Minjiang University, Fuzhou, Fujian 350108, China
| | - Liu Hong
- School of Mathematics, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Lee Jia
- Institute of Oceanography, Minjiang University, Fuzhou, Fujian 350108, China
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37
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Danial JSH, Klenerman D. Single molecule imaging of protein aggregation in Dementia: Methods, insights and prospects. Neurobiol Dis 2021; 153:105327. [PMID: 33705938 PMCID: PMC8039184 DOI: 10.1016/j.nbd.2021.105327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/21/2021] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
The aggregation of misfolded proteins is a fundamental pathology in neurodegeneration which remains poorly understood due to its exceptional complexity and lack of appropriate characterization tools that can probe the role of the low concentrations of heterogeneous protein aggregates formed during the progression of the disease. In this review, we explain the principles underlying the operation of single molecule microscopy, an imaging method that can resolve molecules one-by-one, its application to imaging and characterizing individual protein aggregates in human samples and in vitro as well as the important questions in neurobiology this has answered and can answer.
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Affiliation(s)
- John S H Danial
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom; UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom.
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom; UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom.
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38
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Jin Y, Vadukul DM, Gialama D, Ge Y, Thrush R, White JT, Aprile FA. The Diagnostic Potential of Amyloidogenic Proteins. Int J Mol Sci 2021; 22:4128. [PMID: 33923609 PMCID: PMC8074075 DOI: 10.3390/ijms22084128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Neurodegenerative disorders are a highly prevalent class of diseases, whose pathological mechanisms start before the appearance of any clear symptoms. This fact has prompted scientists to search for biomarkers that could aid early treatment. These currently incurable pathologies share the presence of aberrant aggregates called amyloids in the nervous system, which are composed of specific proteins. In this review, we discuss how these proteins, their conformations and modifications could be exploited as biomarkers for diagnostic purposes. We focus on proteins that are associated with the most prevalent neurodegenerative disorders, including Alzheimer's and Parkinson's diseases, amyotrophic lateral sclerosis, and frontotemporal dementia. We also describe current challenges in detection, the most recent techniques with diagnostic potentials and possible future developments in diagnosis.
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Affiliation(s)
| | | | | | | | | | | | - Francesco Antonio Aprile
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK; (Y.J.); (D.M.V.); (D.G.); (Y.G.); (R.T.); (J.T.W.)
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39
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Mei J, Yang H, Sun B, Liu C, Ai H. Small-Molecule Targeted Aβ 42 Aggregate Degradation: Negatively Charged Small Molecules Are More Promising than the Neutral Ones. ACS Chem Neurosci 2021; 12:1197-1209. [PMID: 33687193 DOI: 10.1021/acschemneuro.1c00047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Heavy evidence has confirmed that Aβ42 oligomers are the most neurotoxic aggregates and play a critical role in the occurrence and development of Alzheimer's disease by causing functional neuron death, cognitive damage, and dementia. Disordered Aβ42 oligomers are challenging therapeutic targets, and no drug is currently in clinical use that modifies the properties of their monomeric states. Here, a negatively charged molecule (ER), rather than the neutral TS1 one, is identified by a molecular dynamics simulation method to be more capable of binding and sequestering the intrinsically disordered amyloid-β peptide Aβ42 in its soluble pentameric state as well as its monomeric components. Results reveal that the ERs interact with Aβ and inhibit the primary nucleation pathways in its aggregation process in entropic expansion mechanism for both Aβ42 and Aβ40 oligomers but with opposite characteristics of hydrophobic surface area (HSA). The interaction between Aβ42 oligomer and either charged ER or neutral TS1/TS0 characterizes decreased HSA, and the decrease in ER-involved case is highly visible, consistent with the observations from in silico and in vitro studies. By contrast, the presence of these inhibitors causes the HSA of Aβ40 oligomer to change undetectably and there is even a bit of increase in the histidine isomerized Aβ40 oligomer. The HSA distinction between Aβ42 and Aβ40 oligomer is possibly derived from the different effects of M35-inhibitor interaction, which is analogous to the effect of M35 oxidation. In comparison with the neutral TS1/TS0 inhibitors, ER is more prone to bind the residues located in the central (β1) and C-terminal (β2) regions of Aβ42 peptide, two key nucleation regions for Aβ intramolecular folding, intermolecular aggregation, and assembly. Notably, ER can strongly bind the charged residues, such as K16, K28, D23, to greatly disturb the potential stabilizer (e.g., salt-bridge, etc.) in metastable Aβ42 oligomers and protofibrils. These results illustrate the strategy of overcoming Alzheimer's disease from inhibiting its early stage Aβ aggregation with two kinds of small molecules to alter their behavior for therapeutic purposes and strongly recommend paying more attention to the engineering and development of negatively charged inhibitors, the long-term underappreciated ones, targeting the early stage Aβ aggregates.
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Affiliation(s)
- Jinfei Mei
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Huijuan Yang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Bo Sun
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Chengqiang Liu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
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40
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Perni M, van der Goot A, Limbocker R, van Ham TJ, Aprile FA, Xu CK, Flagmeier P, Thijssen K, Sormanni P, Fusco G, Chen SW, Challa PK, Kirkegaard JB, Laine RF, Ma KY, Müller MBD, Sinnige T, Kumita JR, Cohen SIA, Seinstra R, Kaminski Schierle GS, Kaminski CF, Barbut D, De Simone A, Knowles TPJ, Zasloff M, Nollen EAA, Vendruscolo M, Dobson CM. Comparative Studies in the A30P and A53T α-Synuclein C. elegans Strains to Investigate the Molecular Origins of Parkinson's Disease. Front Cell Dev Biol 2021; 9:552549. [PMID: 33829010 PMCID: PMC8019828 DOI: 10.3389/fcell.2021.552549] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/16/2021] [Indexed: 02/02/2023] Open
Abstract
The aggregation of α-synuclein is a hallmark of Parkinson's disease (PD) and a variety of related neurological disorders. A number of mutations in this protein, including A30P and A53T, are associated with familial forms of the disease. Patients carrying the A30P mutation typically exhibit a similar age of onset and symptoms as sporadic PD, while those carrying the A53T mutation generally have an earlier age of onset and an accelerated progression. We report two C. elegans models of PD (PDA30P and PDA53T), which express these mutational variants in the muscle cells, and probed their behavior relative to animals expressing the wild-type protein (PDWT). PDA30P worms showed a reduced speed of movement and an increased paralysis rate, control worms, but no change in the frequency of body bends. By contrast, in PDA53T worms both speed and frequency of body bends were significantly decreased, and paralysis rate was increased. α-Synuclein was also observed to be less well localized into aggregates in PDA30P worms compared to PDA53T and PDWT worms, and amyloid-like features were evident later in the life of the animals, despite comparable levels of expression of α-synuclein. Furthermore, squalamine, a natural product currently in clinical trials for treating symptomatic aspects of PD, was found to reduce significantly the aggregation of α-synuclein and its associated toxicity in PDA53T and PDWT worms, but had less marked effects in PDA30P. In addition, using an antibody that targets the N-terminal region of α-synuclein, we observed a suppression of toxicity in PDA30P, PDA53T and PDWT worms. These results illustrate the use of these two C. elegans models in fundamental and applied PD research.
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Affiliation(s)
- Michele Perni
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Annemieke van der Goot
- University Medical Centre Groningen, European Research Institute for the Biology of Aging, University of Groningen, Groningen, Netherlands
| | - Ryan Limbocker
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom,Department of Chemistry and Life Science, United States Military Academy, West Point, NY, United States
| | - Tjakko J. van Ham
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Francesco A. Aprile
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Catherine K. Xu
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Patrick Flagmeier
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Karen Thijssen
- University Medical Centre Groningen, European Research Institute for the Biology of Aging, University of Groningen, Groningen, Netherlands
| | - Pietro Sormanni
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Giuliana Fusco
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Serene W. Chen
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Pavan K. Challa
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Julius B. Kirkegaard
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom
| | - Romain F. Laine
- MRC Laboratory for Molecular Cell Biology (LMCB) University College London, London, United Kingdom
| | - Kai Yu Ma
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom,University Medical Centre Groningen, European Research Institute for the Biology of Aging, University of Groningen, Groningen, Netherlands
| | - Martin B. D. Müller
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom,University Medical Centre Groningen, European Research Institute for the Biology of Aging, University of Groningen, Groningen, Netherlands
| | - Tessa Sinnige
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Janet R. Kumita
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Samuel I. A. Cohen
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Renée Seinstra
- University Medical Centre Groningen, European Research Institute for the Biology of Aging, University of Groningen, Groningen, Netherlands
| | | | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Denise Barbut
- MedStar-Georgetown Transplant Institute, Georgetown University School of Medicine, Washington, DC, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Tuomas P. J. Knowles
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Michael Zasloff
- MedStar-Georgetown Transplant Institute, Georgetown University School of Medicine, Washington, DC, United States
| | - Ellen A. A. Nollen
- University Medical Centre Groningen, European Research Institute for the Biology of Aging, University of Groningen, Groningen, Netherlands,*Correspondence: Ellen A. A. Nollen
| | - Michele Vendruscolo
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom,Michele Vendruscolo
| | - Christopher M. Dobson
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
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41
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Gomes GN, Levine ZA. Defining the Neuropathological Aggresome across in Silico, in Vitro, and ex Vivo Experiments. J Phys Chem B 2021; 125:1974-1996. [PMID: 33464098 PMCID: PMC8362740 DOI: 10.1021/acs.jpcb.0c09193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The loss of proteostasis over the life course is associated with a wide range of debilitating degenerative diseases and is a central hallmark of human aging. When left unchecked, proteins that are intrinsically disordered can pathologically aggregate into highly ordered fibrils, plaques, and tangles (termed amyloids), which are associated with countless disorders such as Alzheimer's disease, Parkinson's disease, type II diabetes, cancer, and even certain viral infections. However, despite significant advances in protein folding and solution biophysics techniques, determining the molecular cause of these conditions in humans has remained elusive. This has been due, in part, to recent discoveries showing that soluble protein oligomers, not insoluble fibrils or plaques, drive the majority of pathological processes. This has subsequently led researchers to focus instead on heterogeneous and often promiscuous protein oligomers. Unfortunately, significant gaps remain in how to prepare, model, experimentally corroborate, and extract amyloid oligomers relevant to human disease in a systematic manner. This Review will report on each of these techniques and their successes and shortcomings in an attempt to standardize comparisons between protein oligomers across disciplines, especially in the context of neurodegeneration. By standardizing multiple techniques and identifying their common overlap, a clearer picture of the soluble neuropathological aggresome can be constructed and used as a baseline for studying human disease and aging.
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Affiliation(s)
- Gregory-Neal Gomes
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Zachary A. Levine
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
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42
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Ikenoue T, Aprile FA, Sormanni P, Vendruscolo M. Rationally Designed Bicyclic Peptides Prevent the Conversion of Aβ42 Assemblies Into Fibrillar Structures. Front Neurosci 2021; 15:623097. [PMID: 33716651 PMCID: PMC7947257 DOI: 10.3389/fnins.2021.623097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/01/2021] [Indexed: 12/27/2022] Open
Abstract
There is great interest in drug discovery programs targeted at the aggregation of the 42-residue form of the amyloid β peptide (Aβ42), since this molecular process is closely associated with Alzheimer’s disease. The use of bicyclic peptides may offer novel opportunities for the effective modification of Aβ42 aggregation and the inhibition of its cytotoxicity, as these compounds combine the molecular recognition ability of antibodies with a relatively small size of about 2 kD. Here, to pursue this approach, we rationally designed a panel of six bicyclic peptides targeting various epitopes along the sequence of Aβ42 to scan its most amyloidogenic region (residues 13–42). Our kinetic analysis and structural studies revealed that at sub-stoichiometric concentrations the designed bicyclic peptides induce a delay in the condensation of Aβ42 and the subsequent transition to a fibrillar state, while at higher concentrations they inhibit such transition. We thus suggest that designed bicyclic peptides can be employed to inhibit amyloid formation by redirecting the aggregation process toward amorphous assemblies.
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Affiliation(s)
- Tatsuya Ikenoue
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Francesco A Aprile
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.,Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, United Kingdom
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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43
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Kulenkampff K, Wolf Perez AM, Sormanni P, Habchi J, Vendruscolo M. Quantifying misfolded protein oligomers as drug targets and biomarkers in Alzheimer and Parkinson diseases. Nat Rev Chem 2021; 5:277-294. [PMID: 37117282 DOI: 10.1038/s41570-021-00254-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
Protein misfolding and aggregation are characteristic of a wide range of neurodegenerative disorders, including Alzheimer and Parkinson diseases. A hallmark of these diseases is the aggregation of otherwise soluble and functional proteins into amyloid aggregates. Although for many decades such amyloid deposits have been thought to be responsible for disease progression, it is now increasingly recognized that the misfolded protein oligomers formed during aggregation are, instead, the main agents causing pathological processes. These oligomers are transient and heterogeneous, which makes it difficult to detect and quantify them, generating confusion about their exact role in disease. The lack of suitable methods to address these challenges has hampered efforts to investigate the molecular mechanisms of oligomer toxicity and to develop oligomer-based diagnostic and therapeutic tools to combat protein misfolding diseases. In this Review, we describe methods to quantify misfolded protein oligomers, with particular emphasis on diagnostic applications as disease biomarkers and on therapeutic applications as target biomarkers. The development of these methods is ongoing, and we discuss the challenges that remain to be addressed to establish measurement tools capable of overcoming existing limitations and to meet present needs.
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44
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Ahmed R, Melacini G. A biophysical toolset to probe the microscopic processes underlying protein aggregation and its inhibition by molecular chaperones. Biophys Chem 2021; 269:106508. [PMID: 33310607 DOI: 10.1016/j.bpc.2020.106508] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/09/2020] [Accepted: 11/13/2020] [Indexed: 10/22/2022]
Abstract
Given the breadth and depth of the scientific contributions of Sir Christopher Dobson, with over 870 publications to date, it is inconceivable to convey in a single review the impact of his work and its legacy. This review therefore primarily focuses on his contributions to the development of strategies for preventing aberrant protein misfolding. The first section of this review highlights his seminal work on the elucidation of the microscopic nucleation processes underlying protein aggregation. Next, we discuss the specific inhibition of these steps by candidate drugs and biologics, with a particular emphasis on the role of molecular chaperones. In the final section, we review how protein aggregation principles can be exploited for the rational design of novel and more potent aggregation inhibitors. These milestones serve as excellent examples of the profound impact of Dobson's seminal work on fundamental science and its translation into drug discovery.
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Affiliation(s)
- Rashik Ahmed
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4M1, Canada; Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada.
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45
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Seuma M, Faure AJ, Badia M, Lehner B, Bolognesi B. The genetic landscape for amyloid beta fibril nucleation accurately discriminates familial Alzheimer's disease mutations. eLife 2021; 10:e63364. [PMID: 33522485 PMCID: PMC7943193 DOI: 10.7554/elife.63364] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/01/2021] [Indexed: 12/20/2022] Open
Abstract
Plaques of the amyloid beta (Aß) peptide are a pathological hallmark of Alzheimer's disease (AD), the most common form of dementia. Mutations in Aß also cause familial forms of AD (fAD). Here, we use deep mutational scanning to quantify the effects of >14,000 mutations on the aggregation of Aß. The resulting genetic landscape reveals mechanistic insights into fibril nucleation, including the importance of charge and gatekeeper residues in the disordered region outside of the amyloid core in preventing nucleation. Strikingly, unlike computational predictors and previous measurements, the empirical nucleation scores accurately identify all known dominant fAD mutations in Aß, genetically validating that the mechanism of nucleation in a cell-based assay is likely to be very similar to the mechanism that causes the human disease. These results provide the first comprehensive atlas of how mutations alter the formation of any amyloid fibril and a resource for the interpretation of genetic variation in Aß.
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Affiliation(s)
- Mireia Seuma
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Andre J Faure
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Marta Badia
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Ben Lehner
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- ICREA, Pg. Lluís CompanysBarcelonaSpain
| | - Benedetta Bolognesi
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and TechnologyBarcelonaSpain
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46
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Lee D, Park D, Kim I, Lee SW, Lee W, Hwang KS, Lee JH, Lee G, Yoon DS. Plasmonic nanoparticle amyloid corona for screening Aβ oligomeric aggregate-degrading drugs. Nat Commun 2021; 12:639. [PMID: 33504788 PMCID: PMC7840768 DOI: 10.1038/s41467-020-20611-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
The generation of toxic amyloid β (Aβ) oligomers is a central feature of the onset and progression of Alzheimer's disease (AD). Drug discoveries for Aβ oligomer degradation have been hampered by the difficulty of Aβ oligomer purification and a lack of screening tools. Here, we report a plasmonic nanoparticle amyloid corona (PNAC) for quantifying the efficacy of Aβ oligomeric aggregate-degrading drugs. Our strategy is to monitor the drug-induced degradation of oligomeric aggregates by analyzing the colorimetric responses of PNACs. To test our strategy, we use Aβ-degrading proteases (protease XIV and MMP-9) and subsequently various small-molecule substances that have shown benefits in the treatment of AD. We demonstrate that this strategy with PNAC can identify effective drugs for eliminating oligomeric aggregates. Thus, this approach presents an appealing opportunity to reduce attrition problems in drug discovery for AD treatment.
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Affiliation(s)
- Dongtak Lee
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
| | - Dongsung Park
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, 02447, South Korea
| | - Insu Kim
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
| | - Sang Won Lee
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea
| | - Wonseok Lee
- Department of Control and Instrumentation Engineering, Korea University, Sejong, 30019, South Korea
| | - Kyo Seon Hwang
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, 02447, South Korea
| | - Jeong Hoon Lee
- Department of Electrical Engineering, Kwangwoon University, Seoul, 01897, South Korea.
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, South Korea.
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong, 30019, South Korea.
| | - Dae Sung Yoon
- School of Biomedical Engineering, Korea University, Seoul, 02841, South Korea.
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, 02841, South Korea.
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47
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Lindstedt PR, Aprile FA, Sormanni P, Rakoto R, Dobson CM, Bernardes GJL, Vendruscolo M. Systematic Activity Maturation of a Single-Domain Antibody with Non-canonical Amino Acids through Chemical Mutagenesis. Cell Chem Biol 2021; 28:70-77.e5. [PMID: 33217338 PMCID: PMC7837213 DOI: 10.1016/j.chembiol.2020.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/03/2020] [Accepted: 11/02/2020] [Indexed: 12/16/2022]
Abstract
Great advances have been made over the last four decades in therapeutic and diagnostic applications of antibodies. The activity maturation of antibody candidates, however, remains a significant challenge. To address this problem, we present a method that enables the systematic enhancement of the activity of a single-domain antibody through the post-translational installation of non-canonical side chains by chemical mutagenesis. We illustrate this approach by performing a structure-activity relationship study beyond the 20 naturally occurring amino acids on a single-domain antibody designed in silico to inhibit the aggregation of the amyloid-β peptide, a process closely linked to Alzheimer's disease. We found that this approach can improve, by five orders of magnitude, the anti-aggregation activity of the starting single-domain antibody, without affecting its stability. These results show that the expansion of the chemical space available to antibodies through chemical mutagenesis can be exploited for the systematic enhancement of the activity of these molecules.
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Affiliation(s)
- Philip R Lindstedt
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK
| | - Francesco A Aprile
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK; Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK
| | - Robertinah Rakoto
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK
| | - Gonçalo J L Bernardes
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Protugal.
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK.
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48
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Kreiser RP, Wright AK, Block NR, Hollows JE, Nguyen LT, LeForte K, Mannini B, Vendruscolo M, Limbocker R. Therapeutic Strategies to Reduce the Toxicity of Misfolded Protein Oligomers. Int J Mol Sci 2020; 21:ijms21228651. [PMID: 33212787 PMCID: PMC7696907 DOI: 10.3390/ijms21228651] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
The aberrant aggregation of proteins is implicated in the onset and pathogenesis of a wide range of neurodegenerative disorders, including Alzheimer’s and Parkinson’s diseases. Mounting evidence indicates that misfolded protein oligomers produced as intermediates in the aggregation process are potent neurotoxic agents in these diseases. Because of the transient and heterogeneous nature of these elusive aggregates, however, it has proven challenging to develop therapeutics that can effectively target them. Here, we review approaches aimed at reducing oligomer toxicity, including (1) modulating the oligomer populations (e.g., by altering the kinetics of aggregation by inhibiting, enhancing, or redirecting the process), (2) modulating the oligomer properties (e.g., through the size–hydrophobicity–toxicity relationship), (3) modulating the oligomer interactions (e.g., by protecting cell membranes by displacing oligomers), and (4) reducing oligomer toxicity by potentiating the protein homeostasis system. We analyze examples of these complementary approaches, which may lead to the development of compounds capable of preventing or treating neurodegenerative disorders associated with protein aggregation.
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Affiliation(s)
- Ryan P. Kreiser
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA; (R.P.K.); (A.K.W.); (N.R.B.); (J.E.H.); (L.T.N.); (K.L.)
| | - Aidan K. Wright
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA; (R.P.K.); (A.K.W.); (N.R.B.); (J.E.H.); (L.T.N.); (K.L.)
| | - Natalie R. Block
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA; (R.P.K.); (A.K.W.); (N.R.B.); (J.E.H.); (L.T.N.); (K.L.)
| | - Jared E. Hollows
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA; (R.P.K.); (A.K.W.); (N.R.B.); (J.E.H.); (L.T.N.); (K.L.)
| | - Lam T. Nguyen
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA; (R.P.K.); (A.K.W.); (N.R.B.); (J.E.H.); (L.T.N.); (K.L.)
| | - Kathleen LeForte
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA; (R.P.K.); (A.K.W.); (N.R.B.); (J.E.H.); (L.T.N.); (K.L.)
| | - Benedetta Mannini
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK;
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK;
- Correspondence: (M.V.); (R.L.)
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA; (R.P.K.); (A.K.W.); (N.R.B.); (J.E.H.); (L.T.N.); (K.L.)
- Correspondence: (M.V.); (R.L.)
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49
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Cawood EE, Karamanos TK, Wilson AJ, Radford SE. Visualizing and trapping transient oligomers in amyloid assembly pathways. Biophys Chem 2020; 268:106505. [PMID: 33220582 PMCID: PMC8188297 DOI: 10.1016/j.bpc.2020.106505] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 12/31/2022]
Abstract
Oligomers which form during amyloid fibril assembly are considered to be key contributors towards amyloid disease. However, understanding how such intermediates form, their structure, and mechanisms of toxicity presents significant challenges due to their transient and heterogeneous nature. Here, we discuss two different strategies for addressing these challenges: use of (1) methods capable of detecting lowly-populated species within complex mixtures, such as NMR, single particle methods (including fluorescence and force spectroscopy), and mass spectrometry; and (2) chemical and biological tools to bias the amyloid energy landscape towards specific oligomeric states. While the former methods are well suited to following the kinetics of amyloid assembly and obtaining low-resolution structural information, the latter are capable of producing oligomer samples for high-resolution structural studies and inferring structure-toxicity relationships. Together, these different approaches should enable a clearer picture to be gained of the nature and role of oligomeric intermediates in amyloid formation and disease. Methods to study structure, toxicity, and kinetics of transient amyloid oligomers. NMR and single particle methods can characterize lowly-populated oligomers. Chemical tools/antibodies stabilize oligomers for structural and toxicity studies A combination of methods is needed to fully characterize amyloid assembly pathways.
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Affiliation(s)
- Emma E Cawood
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK.
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50
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Heller GT, Aprile FA, Michaels TCT, Limbocker R, Perni M, Ruggeri FS, Mannini B, Löhr T, Bonomi M, Camilloni C, De Simone A, Felli IC, Pierattelli R, Knowles TPJ, Dobson CM, Vendruscolo M. Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease. SCIENCE ADVANCES 2020; 6:6/45/eabb5924. [PMID: 33148639 PMCID: PMC7673680 DOI: 10.1126/sciadv.abb5924] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/22/2020] [Indexed: 05/15/2023]
Abstract
Disordered proteins are challenging therapeutic targets, and no drug is currently in clinical use that modifies the properties of their monomeric states. Here, we identify a small molecule (10074-G5) capable of binding and sequestering the intrinsically disordered amyloid-β (Aβ) peptide in its monomeric, soluble state. Our analysis reveals that this compound interacts with Aβ and inhibits both the primary and secondary nucleation pathways in its aggregation process. We characterize this interaction using biophysical experiments and integrative structural ensemble determination methods. We observe that this molecule increases the conformational entropy of monomeric Aβ while decreasing its hydrophobic surface area. We also show that it rescues a Caenorhabditis elegans model of Aβ-associated toxicity, consistent with the mechanism of action identified from the in silico and in vitro studies. These results illustrate the strategy of stabilizing the monomeric states of disordered proteins with small molecules to alter their behavior for therapeutic purposes.
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Affiliation(s)
- Gabriella T Heller
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Francesco A Aprile
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Thomas C T Michaels
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Ryan Limbocker
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Francesco Simone Ruggeri
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Benedetta Mannini
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Thomas Löhr
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Massimiliano Bonomi
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry. CNRS UMR 3528, C3BI, CNRS USR 3756, Institut Pasteur, Paris, France
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Alfonso De Simone
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
- Department of Pharmacy, University of Naples "Federico II," 80131 Naples, Italy
| | - Isabella C Felli
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff," University of Florence, 50019 Sesto Fiorentino, Italy
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff," University of Florence, 50019 Sesto Fiorentino, Italy
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
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