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

Aberrant mitochondrial localization of 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 mislocalization of TDP-43 remains to be investigated. Three internal peptide sequences from TDP-43, M1, M3, and M5, were found to enable TDP-43's mitochondrial localization. The peptides carrying these sequences thwarted mitochondrial import of TDP-43 and rescued TDP-43-induced cytotoxicity to neurons. In the current study, we aimed to assess the repurposing potential of 2115 FDA-approved small molecules for binding to the M3 region of TDP-43 (aa: 146-150) through virtual screening. The M3 region is present in the RNA-recognition motif-1 (RRM-1); hence, multiple all-atom molecular dynamics (MD) simulations, with two different starting conformations, of the tandem RRM1-2 domains of TDP-43 in explicit solvent water were performed to understand the dynamics of the target M3 region. 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), as identified through virtual screening, consistently docked with the M3 region across various docking strategies, despite the region's poor accessibility in most conformations. 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 mislocalization of TDP-43.