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Wallace HM, Yang H, Tan S, Pan HS, Yang R, Xu J, Jo H, Condello C, Polizzi NF, DeGrado WF. De novo design of peptides that bind specific conformers of α-synuclein. Chem Sci 2024; 15:8414-8421. [PMID: 38846390 PMCID: PMC11151861 DOI: 10.1039/d3sc06245g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/14/2024] [Indexed: 06/09/2024] Open
Abstract
Insoluble amyloids rich in cross-β fibrils are observed in a number of neurodegenerative diseases. Depending on the clinicopathology, the amyloids can adopt distinct supramolecular assemblies, termed conformational strains. However, rapid methods to study amyloids in a conformationally specific manner are lacking. We introduce a novel computational method for de novo design of peptides that tile the surface of α-synuclein fibrils in a conformationally specific manner. Our method begins by identifying surfaces that are unique to the conformational strain of interest, which becomes a "target backbone" for the design of a peptide binder. Next, we interrogate structures in the PDB with high geometric complementarity to the target. Then, we identify secondary structural motifs that interact with this target backbone in a favorable, highly occurring geometry. This method produces monomeric helical motifs with a favorable geometry for interaction with the strands of the underlying amyloid. Each motif is then symmetrically replicated to form a monolayer that tiles the amyloid surface. Finally, amino acid sequences of the peptide binders are computed to provide a sequence with high geometric and physicochemical complementarity to the target amyloid. This method was applied to a conformational strain of α-synuclein fibrils, resulting in a peptide with high specificity for the target relative to other amyloids formed by α-synuclein, tau, or Aβ40. This designed peptide also markedly slowed the formation of α-synuclein amyloids. Overall, this method offers a new tool for examining conformational strains of amyloid proteins.
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Affiliation(s)
- Hailey M Wallace
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institution, University of California San Francisco CA 94158 USA
| | - Hyunjun Yang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institution, University of California San Francisco CA 94158 USA
- Institute for Neurodegenerative Diseases, University of California San Francisco CA 94143 USA
| | - Sophia Tan
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institution, University of California San Francisco CA 94158 USA
| | - Henry S Pan
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institution, University of California San Francisco CA 94158 USA
| | - Rose Yang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institution, University of California San Francisco CA 94158 USA
| | - Junyi Xu
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institution, University of California San Francisco CA 94158 USA
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institution, University of California San Francisco CA 94158 USA
| | - Carlo Condello
- Institute for Neurodegenerative Diseases, University of California San Francisco CA 94143 USA
- Department of Neurology, University of California San Francisco CA 94143 USA
| | - Nicholas F Polizzi
- Dana Farber Cancer Institute, Harvard Medical School Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston MA 02215 USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institution, University of California San Francisco CA 94158 USA
- Institute for Neurodegenerative Diseases, University of California San Francisco CA 94143 USA
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Wallace HM, Yang H, Tan S, Pan HS, Yang R, Xu J, Jo H, Condello C, Polizzi NF, DeGrado WF. De novo Design of Peptides that Bind Specific Conformers of α-Synuclein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567090. [PMID: 38014268 PMCID: PMC10680688 DOI: 10.1101/2023.11.14.567090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Insoluble amyloids rich in cross-β fibrils are observed in a number of neurodegenerative diseases. Depending on the clinicopathology, the amyloids can adopt distinct supramolecular assemblies, termed conformational strains. However, rapid methods to study amyloid in a conformationally specific manner are lacking. We introduce a novel computational method for de novo design of peptides that tile the surface of α-synuclein fibrils in a conformationally specific manner. Our method begins by identifying surfaces that are unique to the conformational strain of interest, which becomes a "target backbone" for the design of a peptide binder. Next, we interrogate structures in the PDB database with high geometric complementarity to the target. Then, we identify secondary structural motifs that interact with this target backbone in a favorable, highly occurring geometry. This method produces monomeric helical motifs with a favorable geometry for interaction with the strands of the underlying amyloid. Each motif is then symmetrically replicated to form a monolayer that tiles the amyloid surface. Finally, amino acid sequences of the peptide binders are computed to provide a sequence with high geometric and physicochemical complementarity to the target amyloid. This method was applied to a conformational strain of α-synuclein fibrils, resulting in a peptide with high specificity for the target relative to other amyloids formed by α-synuclein, tau, or Aβ40. This designed peptide also markedly slowed the formation of α-synuclein amyloids. Overall, this method offers a new tool for examining conformational strains of amyloid proteins.
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Aillaud I, Kaniyappan S, Chandupatla RR, Ramirez LM, Alkhashrom S, Eichler J, Horn AHC, Zweckstetter M, Mandelkow E, Sticht H, Funke SA. A novel D-amino acid peptide with therapeutic potential (ISAD1) inhibits aggregation of neurotoxic disease-relevant mutant Tau and prevents Tau toxicity in vitro. Alzheimers Res Ther 2022; 14:15. [PMID: 35063014 PMCID: PMC8783508 DOI: 10.1186/s13195-022-00959-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/06/2022] [Indexed: 12/19/2022]
Abstract
Background Alzheimer’s disease (AD), the most common form of dementia, is a progressive neurodegenerative disorder that mainly affects older adults. One of the pathological hallmarks of AD is abnormally aggregated Tau protein that forms fibrillar deposits in the brain. In AD, Tau pathology correlates strongly with clinical symptoms, cognitive dysfunction, and neuronal death. Methods We aimed to develop novel therapeutic D-amino acid peptides as Tau fibrillization inhibitors. It has been previously demonstrated that D-amino acid peptides are protease stable and less immunogenic than L-peptides, and these characteristics may render them suitable for in vivo applications. Using a phage display procedure against wild type full-length Tau (TauFL), we selected a novel Tau binding L-peptide and synthesized its D-amino acid version ISAD1 and its retro inversed form, ISAD1rev, respectively. Results While ISAD1rev inhibited Tau aggregation only moderately, ISAD1 bound to Tau in the aggregation-prone PHF6 region and inhibited fibrillization of TauFL, disease-associated mutant full-length Tau (TauFLΔK, TauFL-A152T, TauFL-P301L), and pro-aggregant repeat domain Tau mutant (TauRDΔK). ISAD1 and ISAD1rev induced the formation of large high molecular weight TauFL and TauRDΔK oligomers that lack proper Thioflavin-positive β-sheet conformation even at lower concentrations. In silico modeling of ISAD1 Tau interaction at the PHF6 site revealed a binding mode similar to those known for other PHF6 binding peptides. Cell culture experiments demonstrated that ISAD1 and its inverse form are taken up by N2a-TauRDΔK cells efficiently and prevent cytotoxicity of externally added Tau fibrils as well as of internally expressed TauRDΔK. Conclusions ISAD1 and related peptides may be suitable for therapy development of AD by promoting off-pathway assembly of Tau, thus preventing its toxicity. Supplementary Information The online version contains supplementary material available at 10.1186/s13195-022-00959-z.
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Affiliation(s)
- Isabelle Aillaud
- Institute of Bioanalysis, Coburg University of Applied Sciences, Coburg, Germany
| | - Senthilvelrajan Kaniyappan
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn, Bonn, Germany
| | | | - Lisa Marie Ramirez
- Forschungsgruppe Translationale Strukturbiologie, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Göttingen, Germany
| | - Sewar Alkhashrom
- Institut für Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jutta Eichler
- Institut für Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Anselm H C Horn
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Institut für Medizinische Genetik, Universität Zürich, Zürich, Switzerland
| | - Markus Zweckstetter
- Forschungsgruppe Translationale Strukturbiologie, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Göttingen, Germany.,Abteilung für NMR-basierte Strukturbiologie, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
| | - Eckhard Mandelkow
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn, Bonn, Germany.,CAESAR Research Center, Bonn, Germany
| | - Heinrich Sticht
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Susanne Aileen Funke
- Institute of Bioanalysis, Coburg University of Applied Sciences, Coburg, Germany.
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Pandey G, Morla S, Nemade HB, Kumar S, Ramakrishnan V. Modulation of aggregation with an electric field; scientific roadmap for a potential non-invasive therapy against tauopathies. RSC Adv 2019; 9:4744-4750. [PMID: 35514655 PMCID: PMC9060620 DOI: 10.1039/c8ra09993f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/22/2019] [Indexed: 11/21/2022] Open
Abstract
Toxic aggregation of tau protein to neurofibrillary tangles (NFTS) is a central pathological event involved in tauopathies. Inhibition of tau protein aggregation can serve as a straightforward therapeutic strategy. However, tau-based therapeutic solutions are not very common. Phenothiazine methylene blue (tau protein inhibitor) is currently the only drug under phase III clinical trials. In this work, a non-invasive strategy is presented for modulating the aggregation of core peptide segments of tau protein (VQIVYK and VQIINK) by using electric fields of varying strengths. We use thioflavin T staining, tyrosine fluorescence assay, electron microscopy, IR, dynamic and static light scattering, and neuronal toxicity estimation, for verifying the effect of electric field on the aggregation kinetics, morphology, conformational state and cellular toxicity of peptide systems. Our observations suggest that electric field arrests the self-assembly of VQIVYK and VQIINK fibrils thereby reducing the neurotoxicity instigated by them. Based on our observations, we propose a prospective scheme for a futuristic non-invasive therapeutic device.
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Affiliation(s)
- Gaurav Pandey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati-781039 India +91 361 258 2249 +91 361 258 2227
| | - Sudhir Morla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati-781039 India +91 361 258 2249 +91 361 258 2227
| | - Harshal B Nemade
- Department of Electronics and Electrical Engineering, Indian Institute of Technology Guwahati Guwahati-781039 India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati-781039 India +91 361 258 2249 +91 361 258 2227
| | - Vibin Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati-781039 India +91 361 258 2249 +91 361 258 2227
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5
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Pir GJ, Choudhary B, Kaniyappan S, Chandupatla RR, Mandelkow E, Mandelkow EM, Wang Y. Suppressing Tau Aggregation and Toxicity by an Anti-Aggregant Tau Fragment. Mol Neurobiol 2018; 56:3751-3767. [PMID: 30196394 PMCID: PMC6476873 DOI: 10.1007/s12035-018-1326-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/20/2018] [Indexed: 11/24/2022]
Abstract
Tau aggregation is a hallmark of a group of neurodegenerative diseases termed Tauopathies. Reduction of aggregation-prone Tau has emerged as a promising therapeutic approach. Here, we show that an anti-aggregant Tau fragment (F3ΔKPP, residues 258–360) harboring the ΔK280 mutation and two proline substitutions (I277P & I308P) in the repeat domain can inhibit aggregation of Tau constructs in vitro, in cultured cells and in vivo in a Caenorhabditis elegans model of Tau aggregation. The Tau fragment reduced Tau-dependent cytotoxicity in a N2a cell model, suppressed the Tau-mediated neuronal dysfunction and ameliorated the defective locomotion in C. elegans. In vitro the fragment competes with full-length Tau for polyanionic aggregation inducers and thus inhibits Tau aggregation. Our combined in vitro and in vivo results suggest that the anti-aggregant Tau fragment may potentially be used to address the consequences of Tau aggregation in Tauopathies.
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Affiliation(s)
- Ghulam Jeelani Pir
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 27, 53127, Bonn, Germany. .,Max-Planck-Institute for Metabolism Research, Hamburg Outstation, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany.
| | - Bikash Choudhary
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 27, 53127, Bonn, Germany.,Max-Planck-Institute for Metabolism Research, Hamburg Outstation, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Senthilvelrajan Kaniyappan
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 27, 53127, Bonn, Germany.,Max-Planck-Institute for Metabolism Research, Hamburg Outstation, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Ram Reddy Chandupatla
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 27, 53127, Bonn, Germany.,Max-Planck-Institute for Metabolism Research, Hamburg Outstation, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Eckhard Mandelkow
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 27, 53127, Bonn, Germany.,Max-Planck-Institute for Metabolism Research, Hamburg Outstation, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany.,CAESAR Research Center, Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
| | - Eva-Maria Mandelkow
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 27, 53127, Bonn, Germany. .,Max-Planck-Institute for Metabolism Research, Hamburg Outstation, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany. .,CAESAR Research Center, Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.
| | - Yipeng Wang
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 27, 53127, Bonn, Germany. .,Max-Planck-Institute for Metabolism Research, Hamburg Outstation, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany.
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Jong K, Grisanti L, Hassanali A. Hydrogen Bond Networks and Hydrophobic Effects in the Amyloid β30–35 Chain in Water: A Molecular Dynamics Study. J Chem Inf Model 2017; 57:1548-1562. [DOI: 10.1021/acs.jcim.7b00085] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- KwangHyok Jong
- Condensed
Matter and Statistical Physics, International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste 34136, Italy
- Department
of Physics, Kim II Sung University, RyongNam Dong, TaeSong District, Pyongyang, D.P.R., Korea
| | - Luca Grisanti
- Condensed
Matter and Statistical Physics, International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste 34136, Italy
| | - Ali Hassanali
- Condensed
Matter and Statistical Physics, International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
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7
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Hsp90 directly interacts, in vitro, with amyloid structures and modulates their assembly and disassembly. Biochim Biophys Acta Gen Subj 2016; 1860:2598-2609. [DOI: 10.1016/j.bbagen.2016.07.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 01/22/2023]
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8
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 743] [Impact Index Per Article: 82.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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