Elucidating the conformational dynamics of the mitochondrial localization signal, M3, of TDP-43 and accessing potential inhibitors using molecular docking and simulation

Abstract

Aberrant mitochondrial localization of the RNA/DNA-binding protein TDP-43 is implicated in amyotrophic lateral sclerosis (ALS) which may affect mitochondrial dynamics and contribute to neuronal toxicity. Inhibitors of the cytoplasmic aggregation of TDP-43 were reported previously, but their effect on the mitochondrial mis-localization of TDP-43 and the mitochondrial function remains to be investigated. Three internal peptide sequences from TDP-43, M1, M3, and M5, were found to enable TDP-43s mitochondrial localization and competitive inhibition using these peptides thwarted mitochondrial import of TDP-43 and rescued TDP-43-induced cytotoxicity to neurons. Here, we performed a virtual in silico screening of 2,115 FDA-approved small molecules for affinity against the M3 region of TDP-43 (aa: 146 - 150) that lies in the RNA recognition motif-1 (RRM1) domain. Multiple all-atom MD simulations were carried out starting with two different conformations of the tandem RRMs to understand the dynamics of the target M3 region in explicit solvent water. The analysis of the simulation trajectories suggests that the M3 region is relatively non-flexible and buried relative to the other regions of the tandem RRM1-2 domains. Cholecalciferol (Vitamin D3), from virtual screening, docked consistently with the M3 region in different docking strategies even amidst the regions poor solvent accessibility. Vitamin D3 also remained stably bound to the M3 region in most frames of four replica MD simulations, each of one microsecond. Taken together, our study proposes vitamin D3 as a potential binder to the M3 region which may inhibit the pathogenic mitochondrial mis-localization of TDP-43.