NMR-Guided Studies to Establish the Binding Interaction between a Peptoid and Protein

Area of Science:

• Biochemistry
• Structural Biology
• Drug Discovery

Background:

• Peptoids, oligomers of N-substituted glycine, offer structural diversity for ligand discovery but pose challenges in determining binding poses.
• Poor solubility of screening hits like peptoid KDT-11 hinders drug discovery progress by limiting in vitro characterization.

Purpose of the Study:

• To overcome solubility limitations of peptoid KDT-11 for Rpn-13.
• To elucidate the biologically relevant binding surface of KDT-11.
• To determine the conformationally stable binding pose of KDT-11 to Rpn-13.

Main Methods:

• Addition of a solubility tag to KDT-11 to enable characterization.
• Structure-activity relationship (SAR) studies and biophysical methods.
• NMR paramagnetic relaxation data integrated with molecular dynamics (MD) simulations for structural modeling.

Main Results:

• A solubility-tagged KDT-11 facilitated detailed structural and biophysical studies.
• MD simulations confirmed a stable peptoid-protein complex structure (>1 μs).
• KDT-11 was found to bind across specific strands and an alpha-helix of Rpn-13, revealing a potential inhibition interface.

Conclusions:

• The methodology enables detailed structural analysis of challenging, flexible ligands like peptoids.
• The identified binding interface on Rpn-13 offers a target for computational drug discovery of more potent inhibitors.
• This approach is extendable to other flexible peptoid or peptide ligands.