NMR Fragment-Based Screening against Tandem RNA Recognition Motifs of TDP-43

Abstract

The TDP-43 is originally a nuclear protein but translocates to the cytoplasm in the pathological condition. TDP-43, as an RNA-binding protein, consists of two RNA Recognition Motifs (RRM1 and RRM2). RRMs are known to involve both protein-nucleotide and protein-protein interactions and mediate the formation of stress granules. Thus, they assist the entire TDP-43 protein with participating in neurodegenerative and cancer diseases. Consequently, they are potential therapeutic targets. Protein-observed and ligand-observed nuclear magnetic resonance (NMR) spectroscopy were used to uncover the small molecule inhibitors against the tandem RRM of TDP-43. We identified three hits weakly binding the tandem RRMs using the ligand-observed NMR fragment-based screening. The binding topology of these hits is then depicted by chemical shift perturbations (CSP) of the 15N-labeled tandem RRM and RRM2, respectively, and modeled by the CSP-guided High Ambiguity Driven biomolecular DOCKing (HADDOCK). These hits mainly bind to the RRM2 domain, which suggests the druggability of the RRM2 domain of TDP-43. These hits also facilitate further studies regarding the hit-to-lead evolution against the TDP-43 RRM domain.

Direct targeting of TDP-43, from small molecules to biologics: the therapeutic landscape

“…Despite its lack of traditional targetable pockets, we and others have shown the ability of small molecules to bind TDP-43, albeit with a rather low affinity 47,49,53 . SAR studies focusing on improving the affinity of existing compounds will reveal how effective these strategies are by increasing potency without increasing off-targeting.…”

“…nTRD22 (green, stick and balls representation) binds to TDP-43 NTD and allosterically modulates residues implicated in nucleic acid binding (pink, stick and balls representation) to disrupt the binding. D. Fragment compounds found to bind TDP-43 53 . E. Fragments are able to bind a pocket in TDP-43 RRM2 domain (red, stick and balls representation).…”

“…Other than our studies, an effort to find molecules targeting TDP-43 using a fragmentbased NMR study identified hits that bound to the RRM domain 53 . Three different NMR techniques were used, saturation transfer difference (STD), water ligand observed via gradient spectroscopy (WaterLOGSY) and Carr-Purcell-Meiboom-Gill (CPMG), to screen 89 cocktails, each containing 10 small molecules.…”

Targeting TDP‐43 proteinopathy with drugs and drug‐like small molecules

“…This compound is a purinergic antagonist. It has been reported that a fragile X (Fmr1) mice models treated with suramin displayed a significant decrease in TDP-43 expression in their synaptosomes (Naviaux et al, 2015).…”

“…In this respect, it is interesting to note that some recent studies have taken the approach of designing drugs based on TDP‐43 structure. For example, using NMR‐based screenings, low MW compounds have been identified that are capable of specifically targeting portions of TDP‐43 such as the tandem RRM motifs (Nshogoza et al, 2019). Another similar search for compounds able to bind the RRM regions of TDP‐43 has allowed the recent discovery of a small molecule that can interfere with C9orf72 but nor UG‐RNA binding called rTRD01.…”