Computational Exploration of the Molecular Mechanism of Epigallocatechin Gallate against TDP-43 Aggregation

Cytoplasmic accumulation of the transactive response deoxyribonucleic acid (DNA)-binding protein of 43 kDa (TDP-43) aggregates represents the primary pathological hallmark of TDP-43 proteinopathies including amyotrophic lateral sclerosis (ALS) and chronic traumatic encephalopathy (CTE). Inhibiting TDP-43 aggregation or disrupting its preformed fibrils might be promising strategies to prevent or delay the development of TDP-43 proteinopathies. Recently, the green tea polyphenol, epigallocatechin gallate (EGCG), was observed to prevent the formation of TDP-43 oligomeric species and fibrillar aggregates. Nevertheless, the atomic-level mechanism of this inhibition has been incompletely characterized. In this study, we performed a multitude of replica exchange with solute tempering 2 (REST2) and all-atom molecular dynamics (MD) simulations of 46.8 μs in total on TDP-43 models with and without EGCG. The REST2 simulation results revealed that EGCG impedes the β-sheet structure formation and interferes the interchain interaction of TDP-43_304-348 dimer. Subsequent analyses show that EGCG could alter the distribution of free energy landscape and hinder the residue-residue interaction of the dimer. The binding analyses confirmed that EGCG preferentially bound to M307, F313, F316, W334, M339, Q344, and Q346 residues, and hydrophobic, polar, and π-π stacking interactions dominate the binding of EGCG on the dimer. Additional conventional molecular dynamics (MD) simulations demonstrated that the protofibrillar tetramer is the minimal stable TDP-43_304-348 protofibril. Taking the tetramer as a protofibril model, we found that EGCG could reduce the structural stability and disrupt the β-sheet structure of TDP-43_304-348 protofibril, thus possessing a destabilization effect on its higher-order structure. This investigation unveils the atomic-level mechanism by which EGCG against TDP-43 aggregation, which may provide potential fundamental knowledge of therapeutic strategies for TDP-43 proteinopathies.