Strategies in the design and development of (TAR) DNA-binding protein 43 (TDP-43) binding ligands

Rao, Praveen P.N.; Shakeri, Arash; Zhao, Yusheng; Calon, Frédéric

doi:10.1016/j.ejmech.2021.113753

Cited by 3 publications

(2 citation statements)

References 131 publications

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“…TDP‐43 is a 414‐residue protein consisting of an N‐terminal domain (NTD, residues 1–76), two RNA recognition motifs (RRM1, residues 106–176; RRM2, residues 191–259), and a C‐terminal domain (CTD, residues 274–414). While the first three domains are folded and their structures have been determined using solution NMR spectroscopy or X‐ray crystallography, 15 the CTD consists of a prion‐like glutamine/asparagine‐rich (Q/N) region (residues 345–366), a glycine‐rich region (residues 366–414) and is intrinsically disordered with an amphipathic helix spanning approximately residues 320–340 16,17 . TDP‐43 also contains a nuclear localization signal (NLS, residues 82–98) and a nuclear export signal (NES, residues 239–250), and is known to have a nuclear localization but also to shuttle between the nucleus and the cytosol 18 .…”

Section: Introductionmentioning

confidence: 99%

Biophysical characterization of full‐length TAR DNA‐binding protein (TDP‐43) phase separation

et al. 2022

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Amyotrophic lateral sclerosis and frontotemporal lobar degeneration with ubiquitin-positive inclusions are associated with deposition of cytosolic inclusion bodies of TAR DNA-binding protein 43 (TDP-43) in brain and motor neurons. We induced phase separation of purified full-length TDP-43 devoid of large tags using a solution-jump method, and monitored it with an array of biophysical techniques. The tetramethylrhodamine-5-maleimide-or Alexa488-labeled protein formed rapidly (<1 min) apparently round, homogeneous and 0.5-1.0 μm wide assemblies, when imaged using confocal fluorescence, bright-field, and stimulated emission depletion microscopy. The assemblies, however, had limited internal diffusion, as assessed with fluorescence recovery after photobleaching, and did not coalesce, but rather clustered into irregular bunches, unlike those formed by the C-terminal domain. They were enriched with α-helical structure, with minor contributions of β-sheet/random structure, had a red-shifted tryptophan fluorescence and did not bind thioflavin T. By monitoring with turbidimetry both the formation of the spherical species and their further clustering under different experimental conditions, we carried out a multiparametric analysis of the two phenomena. In particular, both processes were found to be promoted by high protein concentrations, salts, crowding agents, weakly by reducing agents, as the pH approached a value of 6.0 from either side (corresponding to the TDP-43 isoionic point), and as the temperature approached a value of 31 C from either side. Important differences were found with respect to the TDP-43 Cterminal domain. Our multiparametric results also provide explanations to some

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Section: Introductionmentioning

confidence: 99%

Biophysical characterization of full‐length TAR DNA‐binding protein (TDP‐43) phase separation

et al. 2022

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“…To our knowledge, there are currently no reported ALS relevant PROTACs, which could be used to target protein (mutant SOD-1 or TDP-43, for example) aggregates found in ALS patients. Rao et al (2021) summarized the current landscape of TDP-43 ligands for the different domains of TDP-43. Solved crystal structures of TDP-43 have enabled the development of TDP-43 ligands.…”

Section: Future Directionsmentioning

confidence: 99%

Exploration of Aberrant E3 Ligases Implicated in Alzheimer’s Disease and Development of Chemical Tools to Modulate Their Function

Potjewyd

Axtman

2021

Front. Cell. Neurosci.

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The Ubiquitin Proteasome System (UPS) is responsible for the degradation of misfolded or aggregated proteins via a multistep ATP-dependent proteolytic mechanism. This process involves a cascade of ubiquitin (Ub) transfer steps from E1 to E2 to E3 ligase. The E3 ligase transfers Ub to a targeted protein that is brought to the proteasome for degradation. The inability of the UPS to remove misfolded or aggregated proteins due to UPS dysfunction is commonly observed in neurodegenerative diseases, such as Alzheimer’s disease (AD). UPS dysfunction in AD drives disease pathology and is associated with the common hallmarks such as amyloid-β (Aβ) accumulation and tau hyperphosphorylation, among others. E3 ligases are key members of the UPS machinery and dysfunction or changes in their expression can propagate other aberrant processes that accelerate AD pathology. The upregulation or downregulation of expression or activity of E3 ligases responsible for these processes results in changes in protein levels of E3 ligase substrates, many of which represent key proteins that propagate AD. A powerful way to better characterize UPS dysfunction in AD and the role of individual E3 ligases is via the use of high-quality chemical tools that bind and modulate specific E3 ligases. Furthermore, through combining gene editing with recent advances in 3D cell culture, in vitro modeling of AD in a dish has become more relevant and possible. These cell-based models of AD allow for study of specific pathways and mechanisms as well as characterization of the role E3 ligases play in driving AD. In this review, we outline the key mechanisms of UPS dysregulation linked to E3 ligases in AD and highlight the currently available chemical modulators. We present several key approaches for E3 ligase ligand discovery being employed with respect to distinct classes of E3 ligases. Where possible, specific examples of the use of cultured neurons to delineate E3 ligase biology have been captured. Finally, utilizing the available ligands for E3 ligases in the design of proteolysis targeting chimeras (PROTACs) to degrade aberrant proteins is a novel strategy for AD, and we explore the prospects of PROTACs as AD therapeutics.

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Brain PET Imaging

Ward¹,

Ly²,

Raji³

2023

PET Clinics

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Strategies in the design and development of (TAR) DNA-binding protein 43 (TDP-43) binding ligands

Cited by 3 publications

References 131 publications

Biophysical characterization of full‐length TAR DNA‐binding protein (TDP‐43) phase separation

Biophysical characterization of full‐length TAR DNA‐binding protein (TDP‐43) phase separation

Exploration of Aberrant E3 Ligases Implicated in Alzheimer’s Disease and Development of Chemical Tools to Modulate Their Function

Brain PET Imaging

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