Computationally Designed Molecules Modulate ALS-Related Amyloidogenic TDP-43<sub>307–319</sub> Aggregation

Liu, Xikun; Duan, Shuya; Jin, Yingying; Walker, Ethan; Tsao, Michelle; Jang, Joshua H.; Chen, Ziying; Singh, Ambuj K.; Cantrell, Kristi Lazar; Ingolfsson, Helgi I.; Buratto, Steven K.; Bowers, Michael T.

doi:10.1021/acschemneuro.3c00582

Cited by 2 publications

(1 citation statement)

References 69 publications

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“…Such studies have been carried out in vitro using different model systems and targeting the aggregation of different domains of TDP-43 using ligands such as nTRD22, poly-ADP-Ribose (PAR), the drug mitoxantrone and 8-hydroxyquinoline-based small molecules [10–13]. Additionally, in silico approaches towards design of inhibitors towards TDP-43 aggregation are also being strategized [14,15]. Previously, we found an imidazole containing acridine derivative, AIM4, that could prevent the in vitro aggregation of a C-terminal fragment of TDP-43, termed TDP-43 2C [16].…”

Section: Introductionmentioning

confidence: 99%

In silicoandin vitrostudies suggest epigallocatechin gallate (EGCG), a polyphenol in green tea, can bind and modulate the aggregation and cytotoxicity of the full-length TDP-43 protein implicated in TDP-43 proteinopathies

Meshram,

Balaji,

Saravanan

et al. 2023

Preprint

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Misfolding and aggregation of TDP-43 protein are implicated in several proteinopathies like ALS and FTLD. Extracellular TDP-43 is also proposed to propagate in a prion-like pathogenic manner to the neighbouring cells. Here, using turbidity and sedimentation assay, we show that a polyphenol in green tea, epigallocatechin gallate (EGCG), can inhibit thein vitroaggregation of the full-length TDP-43 protein. Furthermore, Alexa-Fluor-labelled TDP-43 protein failed to show aggregates in the presence of EGCG in fluorescence microscopy. Also, AFM imaging revealed that EGCG co-incubation with TDP-43 allows formation of only small oligomers in contrast to the larger TDP-43 aggregates formed otherwise. A physical binding of EGCG with TDP-43 was observed using triphenyl tetrazolium chloride (TTC) staining and isothermal titration calorimetry (ITC). ITC also revealed a high-affinity binding site for EGCG on TDP-43 with a Kdvalue of 7.8 µM and a binding free energy of -6.9 kcal/mol. Furthermore,in silicomolecular docking and molecular dynamic simulation (MDS) studies using different available structures of the N-terminal, RRM1-2 and C-terminal domains of TDP-43, predicted a preferable and stable binding of EGCG to the structure of the aggregation prone C-terminal domain (CTD) (PDB ID:7KWZ). Also, EGCG complexed with CTD of TDP-43 yielded a negative ΔG value of -20.29 kcal/mol using MM-PBSA analysis of the MDS data thereby further suggesting a stable complex formation. Also, in MDS, EGCG interacted with the amino acids Phe-313 and Ala-341 of TDP-43, which were previously projected to be important for the recruitment of monomers for the amyloid formation by CTD, thereby suggesting a possible mechanism of EGCG’s inhibition of the TDP-43 aggregation. Notably, while thein vitro-made aggregates of full-length TDP-43 caused mild cytotoxicity to the HEK293 cells, the small oligomers of TDP-43 formed in presence of EGCG did not. In totality, EGCG canin vitrointeract with TDP-43 and inhibit its aggregation, possiblyviainteraction with the amyloidogenic domain, thereby preventing it from assuming cytotoxic conformations. As EGCG is a natural molecule, it could be relevant to the therapeutic quest against the TDP-43 proteinopathies.

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Section: Introductionmentioning

confidence: 99%

In silicoandin vitrostudies suggest epigallocatechin gallate (EGCG), a polyphenol in green tea, can bind and modulate the aggregation and cytotoxicity of the full-length TDP-43 protein implicated in TDP-43 proteinopathies

Meshram,

Balaji,

Saravanan

et al. 2023

Preprint

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Computational Insights Into the Mechanism of EGCG's Binding and Inhibition of the TDP‐43 Aggregation

Meshram,

Balaji,

Saravanan

et al. 2024

Chem Biol Drug Des

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Misfolding and aggregation of TAR DNA‐binding protein, TDP‐43, is linked to devastating proteinopathies such as ALS. Therefore, targeting TDP‐43's aggregation is significant for therapeutics. Recently, green tea polyphenol, EGCG, was observed to promote non‐toxic TDP‐43 oligomer formation disallowing TDP‐43 aggregation. Here, we investigated if the anti‐aggregation effect of EGCG is mediated via EGCG's binding to TDP‐43. In silico molecular docking and molecular dynamics (MD) simulation suggest a strong binding of EGCG with TDP‐43's aggregation‐prone C‐terminal domain (CTD). Three replicas, each having 800 ns MD simulation of the EGCG‐TDP‐43‐CTD complex, yielded a high negative binding free energy (ΔG) inferring a stable complex formation. Simulation snapshots show that EGCG forms close and long‐lasting contacts with TDP‐43's Phe‐313 and Ala‐341 residues, which were previously identified for monomer recruitment in CTD's aggregation. Notably, stable physical interactions between TDP‐43 and EGCG were also detected in vitro using TTC staining and isothermal titration calorimetry which revealed a high‐affinity binding site of EGCG on TDP‐43 (Kd, 7.8 μM; ΔG, −6.9 kcal/mol). Additionally, TDP‐43 co‐incubated with EGCG was non‐cytotoxic when added to HEK293 cells. In summary, EGCG's binding to TDP‐43 and blocking of residues important for aggregation can be a possible mechanism of its anti‐aggregation effects on TDP‐43.

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Computationally Designed Molecules Modulate ALS-Related Amyloidogenic TDP-43_307–319 Aggregation

Cited by 2 publications

References 69 publications

In silicoandin vitrostudies suggest epigallocatechin gallate (EGCG), a polyphenol in green tea, can bind and modulate the aggregation and cytotoxicity of the full-length TDP-43 protein implicated in TDP-43 proteinopathies

In silicoandin vitrostudies suggest epigallocatechin gallate (EGCG), a polyphenol in green tea, can bind and modulate the aggregation and cytotoxicity of the full-length TDP-43 protein implicated in TDP-43 proteinopathies

Computational Insights Into the Mechanism of EGCG's Binding and Inhibition of the TDP‐43 Aggregation

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Computationally Designed Molecules Modulate ALS-Related Amyloidogenic TDP-43307–319 Aggregation

Cited by 2 publications

References 69 publications

In silicoandin vitrostudies suggest epigallocatechin gallate (EGCG), a polyphenol in green tea, can bind and modulate the aggregation and cytotoxicity of the full-length TDP-43 protein implicated in TDP-43 proteinopathies

In silicoandin vitrostudies suggest epigallocatechin gallate (EGCG), a polyphenol in green tea, can bind and modulate the aggregation and cytotoxicity of the full-length TDP-43 protein implicated in TDP-43 proteinopathies

Computational Insights Into the Mechanism of EGCG's Binding and Inhibition of the TDP‐43 Aggregation

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Computationally Designed Molecules Modulate ALS-Related Amyloidogenic TDP-43_307–319 Aggregation