Oligo(N-methylalanine) as a Peptide-Based Molecular Scaffold with a Minimal Structure and High Density of Functionalizable Sites

A high-resolution structural characterization and physicochemical study of how a peptoid binds to an oncoprotein MDM2

Peptoids are a promising drug modality targeting disease-related proteins, but how a peptoid engages in protein binding is poorly understood. This is primarily due to a lack of high-resolution peptoid-protein complex structures and systematic physicochemical studies. Here, we present the first crystal structure of a peptoid bound to a protein, providing high-resolution structural information about how a peptoid binds to a protein. We previously reported a rigid peptoid, oligo(N-substituted alanine) (oligo-NSA), and developed an oligo-NSA-type peptoid that binds to MDM2. X-ray crystallographic analysis of the peptoid bound to MDM2 showed that the peptoid recognizes the MDM2 surface predominantly through the interaction of the N-substituents, while the main chain acts as a scaffold. Additionally, conformational, thermodynamic, and kinetic analysis of the peptoid and its derivatives with a less rigid main chain revealed that rigidification of the peptoid main chain contributes to improving the protein binding affinity. This improvement is thermodynamically attributed to an increased magnitude of the binding enthalpy change, and kinetically to an increased association rate and decreased dissociation rate. This study provides invaluable insights into the design of protein-targeting peptoids.

Quantitative and Nondestructive Colorimetric Amine Detection Method for the Solid-Phase Peptide Synthesis as an Alternative to the Kaiser Test

Solid-phase peptide synthesis (SPPS) is an essential technique for the synthesis of peptide. For half a century, many amine detection methods have been developed to monitor coupling reactions during SPPS. Despite such efforts, to the best of our knowledge, a nondestructive and quantitative colorimetric method has not been developed. Here, we developed the first quantitative and nondestructive colorimetric amine detection method based on an acid-base reaction between HCl salt of electron donor-acceptor type dyes and amino groups on the resin. In this method, a noncolored solution of HCl salt consisting of dyes, whose pKBH+ value was carefully tuned, was deprotonated by amines, allowing the appearance of a yellow color. A good linear relationship (R2 = 0.999) between the absorption of the colored solution and the amine group quantities was confirmed. For all tested proteinogenic and nonproteinogenic amino acids, we achieved quantitative colorimetric analysis with a small relative standard deviation (RSD < 3.6%). Furthermore, during the practical synthesis of an octapeptide containing undetectable amino acids with the Kaiser test, our amine detection allowed for detailed monitoring of the coupling reaction, resulting in a significantly purer peptide in the crude form than that obtained using the Kaiser test.

Residue-based program of a β-peptoid twisted strand shape via a cyclopentane constraint

N-Substituted peptides, such as peptoids and β-peptoids, have been reported to have unique structures with diverse functions, like catalysis and manipulation of biomolecular functions. Recently, the preorganization of monomer shape by restricting bond rotations about all backbone dihedral angles has been demonstrated to be useful for de novo design of peptoid structures. Such design strategies are hitherto unexplored for β-peptoids; to date, no preorganized β-peptoid monomers have been reported. Here, we report the first design strategy for β-peptoids, in which all four backbone dihedral angles (ω, ϕ, θ, ψ) are rotationally restricted on a per-residue basis. The introduction of a cyclopentane constraint realized the preorganized monomer structure and led to a β-peptoid with a stable twisted strand shape.