1
|
Yang L, Jasiqi Y, Zettor A, Vadas O, Chiaravalli J, Agou F, Lashuel HA. Effective Inhibition of TDP-43 Aggregation by Native State Stabilization. Angew Chem Int Ed Engl 2024; 63:e202314587. [PMID: 37949836 DOI: 10.1002/anie.202314587] [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: 10/09/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Abstract
Preventing the misfolding or aggregation of transactive response DNA binding protein with 43 kDa (TDP-43) is the most actively pursued disease-modifying strategy to treat amyotrophic lateral sclerosis and other neurodegenerative diseases. In this work, we provide proof of concept that native state stabilization of TDP-43 is a viable and effective strategy for treating TDP-43 proteinopathies. Firstly, we leveraged the Cryo-EM structures of TDP-43 fibrils to design C-terminal substitutions that disrupt TDP-43 aggregation. Secondly, we showed that these substitutions (S333D/S342D) stabilize monomeric TDP-43 without altering its physiological properties. Thirdly, we demonstrated that binding native oligonucleotide ligands stabilized monomeric TDP-43 and prevented its fibrillization and phase separation in the absence of direct binding to the aggregation-prone C-terminal domain. Fourthly, we showed that the monomeric TDP-43 variant could be induced to aggregate in a controlled manner, which enabled the design and implementation of a high-throughput screening assay to identify native state stabilizers of TDP-43. Altogether, our findings demonstrate that different structural domains in TDP-43 could be exploited and targeted to develop drugs that stabilize the native state of TDP-43 and provide a platform to discover novel drugs to treat TDP-43 proteinopathies.
Collapse
Affiliation(s)
- Lixin Yang
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Rte Cantonale, 1015, Lausanne, Switzerland
| | - Yllza Jasiqi
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Rte Cantonale, 1015, Lausanne, Switzerland
| | - Agnès Zettor
- Chemogenomic and Biological Screening Core Facility, Institut Pasteur, Université Paris Cité, CNRS, UMR 3523, C2RT, Paris, France
| | - Oscar Vadas
- Protein Platform, Faculty of Medicine, University of Geneva, 1 Rue Michel Servet, 1211, Geneva, Switzerland
| | - Jeanne Chiaravalli
- Chemogenomic and Biological Screening Core Facility, Institut Pasteur, Université Paris Cité, CNRS, UMR 3523, C2RT, Paris, France
| | - Fabrice Agou
- Chemogenomic and Biological Screening Core Facility, Institut Pasteur, Université Paris Cité, CNRS, UMR 3523, C2RT, Paris, France
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Rte Cantonale, 1015, Lausanne, Switzerland
| |
Collapse
|
2
|
Liu X, Duan S, Jin Y, Walker E, Tsao M, Jang JH, Chen Z, Singh AK, Cantrell KL, Ingolfsson HI, Buratto SK, Bowers MT. Computationally Designed Molecules Modulate ALS-Related Amyloidogenic TDP-43 307-319 Aggregation. ACS Chem Neurosci 2023; 14:4395-4408. [PMID: 38050862 DOI: 10.1021/acschemneuro.3c00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023] Open
Abstract
Abnormal cytosolic aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) is observed in multiple diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration, and Alzheimer's disease. Previous studies have shown that TDP-43307-319 located at the C-terminal of TDP-43 can form higher-order oligomers and fibrils. Of particular interest are the hexamers that adopt a cylindrin structure that has been strongly correlated to neurotoxicity. In this study, we use the joint pharmacophore space (JPS) model to identify and generate potential TDP-43 inhibitors. Five JPS-designed molecules are evaluated using both experimental and computational methods: ion mobility mass spectrometry, thioflavin T fluorescence assay, circular dichroism spectroscopy, atomic force microscopy, and molecular dynamics simulations. We found that all five molecules can prevent the amyloid fibril formation of TDP-43307-319, but their efficacy varies significantly. Furthermore, among the five molecules, [AC0101] is the most efficient in preventing the formation of higher-order oligomers and dissociating preformed higher-order oligomers. Molecular dynamics simulations show that [AC0101] both is the most flexible and forms the most hydrogen bonds with the TDP-43307-319 monomer. The JPS-designed molecules can insert themselves between the β-strands in the hexameric cylindrin structure of TDP-43307-319 and can open its structure. Possible mechanisms for JPS-designed molecules to inhibit and dissociate TDP-43307-319 oligomers on an atomistic scale are proposed.
Collapse
Affiliation(s)
- Xikun Liu
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Shuya Duan
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Yingying Jin
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Ethan Walker
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Michelle Tsao
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Joshua H Jang
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Ziying Chen
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Ambuj K Singh
- Department of Computer Science, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Kristi Lazar Cantrell
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Helgi I Ingolfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Steven K Buratto
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael T Bowers
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| |
Collapse
|
3
|
Role of Triggers on the Structural and Functional Facets of TAR DNA-binding Protein 43. Neuroscience 2023; 511:110-130. [PMID: 36442745 DOI: 10.1016/j.neuroscience.2022.11.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/15/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
Nuclear TAR DNA-binding protein 43 (TDP-43) mitigates cellular function, but the dynamic nucleus-cytoplasm shuttling of TDP-43 is disrupted in diseases, such as Amyotrophic Lateral Sclerosis (ALS). The polymorphic nature of the TDP-43 structures in vitro and in vivo is a result of environmental factors leading to the protein pathogenesis. Once the triggers which mitigate TDP-43 biochemistry are identified, new therapies can be developed. This review aims to illustrate recent discoveries in the diversity of TDP-43 structures (amyloidogenic and non-amyloidogenic) and highlight the triggers which result in their formation.
Collapse
|
4
|
Liu X, Ganguly P, Jin Y, Jhatro MJ, Shea JE, Buratto SK, Bowers MT. Tachykinin Neuropeptides and Amyloid β (25-35) Assembly: Friend or Foe? J Am Chem Soc 2022; 144:14614-14626. [PMID: 35917596 DOI: 10.1021/jacs.2c03845] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amyloid β (Aβ) protein is responsible for Alzheimer's disease, and one of its important fragments, Aβ(25-35), is found in the brain and has been shown to be neurotoxic. Tachykinin neuropeptides, including Neuromedin K (NK), Kassinin, and Substance P, have been reported to reduce Aβ(25-35)'s toxicity in cells even though they share similar primary structures with Aβ(25-35). Here, we seek to understand the molecular mechanisms of how these peptides interact with Aβ(25-35) and to shed light on why some peptides with similar primary structures are toxic and others nontoxic. We use both experimental and computational methods, including ion mobility mass spectrometry and enhanced-sampling replica-exchange molecular dynamics simulations, to study the aggregation pathways of Aβ(25-35), NK, Kassinin, Substance P, and mixtures of the latter three with Aβ(25-35). NK and Substance P were observed to remove the higher-order oligomers (i.e., hexamers and dodecamers) of Aβ(25-35), which are related to its toxicity, although Substance P did so more slowly. In contrast, Kassinin was found to promote the formation of these higher-order oligomers. This result conflicts with what is expected and is elaborated on in the text. We also observe that even though they have significant structural homology with Aβ(25-35), NK, Kassinin, and Substance P do not form hexamers with a β-sheet structure like Aβ(25-35). The hexamer structure of Aβ(25-35) has been identified as a cylindrin, and this structure has been strongly correlated to toxic species. The reasons why the three tachykinin peptides behave so differently when mixed with Aβ(25-35) are discussed.
Collapse
Affiliation(s)
- Xikun Liu
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Pritam Ganguly
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Yingying Jin
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael J Jhatro
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Steven K Buratto
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael T Bowers
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| |
Collapse
|
5
|
Strategies in the design and development of (TAR) DNA-binding protein 43 (TDP-43) binding ligands. Eur J Med Chem 2021; 225:113753. [PMID: 34388383 DOI: 10.1016/j.ejmech.2021.113753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/16/2021] [Accepted: 08/05/2021] [Indexed: 01/09/2023]
Abstract
The human transactive responsive (TAR) DNA-binding protein 43 (TDP-43) is involved in a number of physiological processes in the body. Its primary function involves RNA regulation. The TDP-43 protein is also involved in many diseases such as amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Alzheimer's disease (AD), Parkinson's disease (PD) and even cancers. These TDP-43 mediated diseases are collectively called as TDP-43 proteinopathies. Intense research in the last decade has increased our understanding on TDP-43 structure and function in biology. The three-dimensional structures of TDP-43 domains such as N-terminal domain (NTD), RNA-recognition motif-1 (RRM1), RNA-recognition motif-2 (RRM2) and the C-terminal domain (CTD) or low-complexity domain (LCD) have been solved. These structures have yielded insights into novel binding sites and pockets at various TDP-43 domains, which can be targeted by designing a diverse library of ligands including small molecules, peptides and oligonucleotides as molecular tools to (i) study TDP-43 function, (ii) develop novel diagnostic agents and (iii) discover disease-modifying therapies to treat TDP-43 proteinopathies. This review provides a summary on recent progress in the development of TDP-43 binding ligands and uses the solved structures of various TDP-43 domains to investigate putative ligand binding regions that can be exploited to discover novel molecular probes to modulate TDP-43 structure and function.
Collapse
|
6
|
Gerbasi VR, Melani RD, Abbatiello SE, Belford MW, Huguet R, McGee JP, Dayhoff D, Thomas PM, Kelleher NL. Deeper Protein Identification Using Field Asymmetric Ion Mobility Spectrometry in Top-Down Proteomics. Anal Chem 2021; 93:6323-6328. [PMID: 33844503 DOI: 10.1021/acs.analchem.1c00402] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Field asymmetric ion mobility spectrometry (FAIMS), when used in proteomics studies, provides superior selectivity and enables more proteins to be identified by providing additional gas-phase separation. Here, we tested the performance of cylindrical FAIMS for the identification and characterization of proteoforms by top-down mass spectrometry of heterogeneous protein mixtures. Combining FAIMS with chromatographic separation resulted in a 62% increase in protein identifications, an 8% increase in proteoform identifications, and an improvement in proteoform identification compared to samples analyzed without FAIMS. In addition, utilization of FAIMS resulted in the identification of proteins encoded by lower-abundance mRNA transcripts. These improvements were attributable, in part, to improved signal-to-noise for proteoforms with similar retention times. Additionally, our results show that the optimal compensation voltage of any given proteoform was correlated with the molecular weight of the analyte. Collectively these results suggest that the addition of FAIMS can enhance top-down proteomics in both discovery and targeted applications.
Collapse
Affiliation(s)
- Vincent R Gerbasi
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States.,Pacific Northwest National Laboratories, Richland, Washington 99352, United States
| | - Rafael D Melani
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| | - Susan E Abbatiello
- Northeastern University, Boston, Massachusetts 02115, United States.,Thermo Fisher Scientific, San Jose, California 98665, United States
| | | | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 98665, United States
| | - John P McGee
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| | - Dawson Dayhoff
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| | - Paul M Thomas
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| |
Collapse
|
7
|
Buratti E. Targeting TDP-43 proteinopathy with drugs and drug-like small molecules. Br J Pharmacol 2020; 178:1298-1315. [PMID: 32469420 DOI: 10.1111/bph.15148] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
Following the discovery of the involvement of the ribonucleoprotein TDP-43 in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD), a major research focus has been to develop treatments that can prevent or alleviate these disease conditions. One pharmacological approach has been to use TDP-43-based disease models to test small molecules and drugs already known to have some therapeutic effect in a variety of neurodegenerative conditions. In parallel, various disease models have been used to perform high-throughput screens of drugs and small compound libraries. The aim of this review will be to provide a general overview of the compounds that have been described to alter pathological characteristics of TDP-43. These include expression levels, cytoplasmic mis-localization, post-translational modifications, cleavage, stress granule recruitment and aggregation. In parallel, this review will also address the use of compounds that modify the autophagic/proteasome systems that are known to target TDP-43 misfolding and aggregation. LINKED ARTICLES: This article is part of a themed issue on Neurochemistry in Japan. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v178.6/issuetoc.
Collapse
Affiliation(s)
- Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| |
Collapse
|