Submonomer Strategy toward Divergent Solid-Phase Synthesis of α-ABpeptoids

cis-Amide promotion in α-ABpeptoid foldamers via triazolium side chains

Precise control of amide bond rotation is crucial for the construction of well-defined three-dimensional structures in peptidomimetic foldamers. We previously introduced α-ABpeptoids as a new class of peptoid foldamers incorporating backbone chirality and demonstrated their folding propensities. However, the rotational isomerism of their backbone amide bonds remains largely unregulated. Here, we report the development of α-ABpeptoids functionalized with triazolium side chains that promote cis-amide bond formation. A series of α-ABpeptoid oligomers bearing neutral triazole or cationic triazolium side chains were synthesized and analyzed by NMR and circular dichroism spectroscopy. The triazolium-functionalized α-ABpeptoids exhibited a strong preference for cis-amide geometry, resulting in enhanced conformational homogeneity. These findings establish triazolium substitution as an effective strategy for conformational control in α-ABpeptoid foldamers, expanding their utility in the design of structured, functional peptidomimetics.

Synthesis and Structural Characterization of Macrocyclic α-ABpeptoids and Their DNA-Encoded Library

The first synthesis of macrocyclic α-ABpeptoids with varying lengths is described. X-ray crystal structures reveal that cyclic trimer displays a chair-like conformation with a cct amide sequence and cyclic tetramer has a saddle-like structure with an uncommon cccc amide arrangement. The creation of a DNA-encoded combinatorial library of macrocyclic α-ABpeptoids is described.

Peptoid-based reprogrammable template for cell-permeable inhibitors of protein-protein interactions

The development of inhibitors of intracellular protein–protein interactions (PPIs) is of great significance for drug discovery, but the generation of a cell-permeable molecule with high affinity to protein is challenging. Oligo(N-substituted glycines) (oligo-NSGs), referred to as peptoids, are attractive as potential intracellular PPI inhibitors owing to their high membrane permeability. However, their intrinsically flexible backbones make the rational design of inhibitors difficult. Here, we propose a peptoid-based rational approach to develop cell-permeable PPI inhibitors using oligo(N-substituted alanines) (oligo-NSAs). The rigid structures of oligo-NSAs enable independent optimization of each N-substituent to improve binding affinity and membrane permeability, while preserving the backbone shape. A molecule with optimized N-substituents inhibited a target PPI in cells, which demonstrated the utility of oligo-NSA as a reprogrammable template to develop intracellular PPI inhibitors.

A peptoid-based modular approach using oligo(N-substituted alanine) as a reprogrammable template enables independent optimization of N-substituents and facile development of cell-permeable inhibitors of protein–protein interactions.

Design and synthesis of a DNA-encoded combinatorial library of bicyclic peptoids

Here we describe the design and synthesis of a DNA-encoded library of bicyclic peptoids. We show that our solid-phase strategy is facile and DNA-compatible, yielding a structurally diverse combinatorial library of bicyclic peptoids of various ring sizes. We also demonstrate that affinity-based screening of a DNA-encoded library of bicyclic peptoids enables to efficiently identify high-affinity ligands for a target protein. Given their highly constraint structures, as well as increased cell permeability and proteolytic stability relative to native peptides, bicyclic peptoids could be an excellent source of protein capture agents. As such, our DNA-encoded library of bicyclic peptoids will serve as versatile tools that facilitate the generation of potent ligands against many challenging targets, such as intracellular protein-protein interactions.

Cell-penetrating, amphipathic cyclic peptoids as molecular transporters for cargo delivery

Here we describe the design, synthesis, and biological evaluation of cell-penetrating, amphipathic cyclic peptoids as a novel class of molecular transporters. We demonstrated that macrocyclization, along with the introduction of hydrophobic residues, greatly enhanced cellular uptake of polyguanidine linear peptoids. The amphipathic cyclic peptoids showed an order of magnitude more efficient intracellular delivery ability, compared to a commonly used polyarginine cell-penetrating peptide, representing one of the best molecular transporters reported to date. Given the excellent cell-permeability, proteolytic stability, and ease of synthesis, the amphipathic cyclic peptoids would be broadly applicable to a wide range of clinical and biological applications.

Fukuyama reduction, Fukuyama coupling and Fukuyama-Mitsunobu alkylation: recent developments and synthetic applications

Fukuyama reaction for the synthesis of multifunctional aldehydes, secondary amines and ketones has gained considerable importance in synthetic organic chemistry because of mild reaction conditions. The use of thioesters in both Fukuyama aldehydes and ketones synthesis is highly attractive for organic chemists as they are easily accessible from corresponding carboxylic acids. Fukuyama-Mitsunobu reaction utilizes 2-nitrobenzenesulfonyl (Ns) for the protection/activation/deprotection of primary amines to afford secondary amines in good yields and high enantioselectivities. This review presents recent synthetic developments and applications of Fukuyama reaction for the synthesis of aldehydes, secondary amines and ketones.

Oligo(β-peptoid)s with Backbone Chirality from Aspartic Acid Derivatives: Synthesis and Property Investigation

Poly(β-peptoid)s (N-substituted poly-β-alanines) are an intriguing class of pseudopeptidic materials for biomedical applications, but the polymers prepared by solution polymerization have restricted diversity and functionality due to synthetic difficulty. Synthesis of structurally diverse poly(β-peptoid)s is highly desirable yet challenging. Herein, we report a new approach to synthesize skeletal chiral β-peptoid polymers from readily available aspartic acid derivatives. Two types of N-substituted β³-homoalanine monomers, i.e., N-(methyl propionate)-Asp-OMe ( ^N MeP-Asp-OMe) and N-(tert-butyl propionate)-Asp-OMe ( ^N tBuP-Asp-OMe), were synthesized in high yield via an aza-Michael addition reaction between l-aspartic acid-1-methyl ester (l-Asp-OMe) and acrylate species. Both N-substituted β³-homoalanines can be readily converted into polymerizable N-substituted β³-homoalanine N-carboxyanhydrides (β-NNCAs). Subsequent ring-opening polymerization (ROP) of these β-NNCA monomers provides access to oligo(β-peptoid)s and mPEG-poly(β-peptoid) diblocks with backbone chirality. Their conformations were preliminarily studied by circular dichroism (CD) spectra and Fourier transform infrared spectroscopy (FT-IR). The synthetic strategy would significantly facilitate the development of novel poly(β-peptoid)s with well-defined and diverse structures.

Per-Residue Program of Multiple Backbone Dihedral Angles of β-Peptoids via Backbone Substitutions

Unique folded structures of natural and synthetic oligomers are the most fundamental basis for their unique functions. N-Substituted β-peptides, or β-peptoids, are synthetic oligomers with great potential to fold into diverse three-dimensional structures because of the existence of four rotatable bonds in a monomer with highly modular synthetic accessibility. However, the existence of the four rotatable bonds poses a challenge for conformational control of β-peptoids. Here, we report a strategy for per-residue programming of two dihedral angles of β-peptoids, which is useful for restricting the conformational space of the oligomers. The oligomer was found to form a unique loop conformation that is stabilized by the backbone rotational restrictions. Circular dichroism and NMR spectroscopic analyses and X-ray crystallographic analysis of the oligomer are presented. The strategy would significantly facilitate the discovery of many more unique folded structures of β-peptoids.

On-Bead Peptoid Dimerization Induced by Incorporation of Glycosylated Bridging Units in Submonomer Solid-Phase Approach to Glycopeptoids

A study on submonomer solid-phase synthesis of S-glycopeptoids has been carried out by screening different parameters. Dimeric species, featuring glycosylated bridging amino monomers, were found under suitable conditions. These dimers arise from an on-resin cross-linking reaction occurring with the incorporation of a glycoamino submonomer into the growing chain and subsequent nucleophilic attack of the resulting secondary amine to a still unreacted bromoacetylated unit. The arising byproduct can be regarded as a novel dimeric peptoid type.

Oligomers of α-ABpeptoid/β3 -peptide hybrid

Peptoids, oligomers of N-substituted glycines, have been attracting increasing interest due to their advantageous properties as peptidomimetics. However, due to the lack of chiral centers and amide hydrogen atoms, peptoids, in general, do not form folding structures except that they have α-chiral side chains. We have recently developed "peptoids with backbone chirality" as a new class of peptoid foldamers called α-ABpeptoids and demonstrated that they could have folding conformations owing to the methyl groups on chiral α-carbons in the backbone structure. Here we report α-ABpeptoid/β³ -peptide oligomers as a unique peptidomimetic structure with a heterogeneous backbone. This hybrid structure contains a mixed α-ABpeptoid and β³ -peptide residues arranged in an alternate manner. These α-ABpeptoid/β³ -peptide oligomers could form intramolecular hydrogen bonding and have better cell permeability relative to pure peptide sequences. These oligomers were shown to adopt ordered folding structures based on circular dichroism studies. Overall, α-ABpeptoid/β³ -peptide oligomers may represent a novel class of peptidomimetic foldamers and will find a wide range of applications in biomedical and material sciences.

Solid-Phase Synthesis and Circular Dichroism Study of β-ABpeptoids

The development of peptidomimetic foldamers that can form well-defined folded structures is highly desirable yet challenging. We previously reported on α-ABpeptoids, oligomers of N-alkylated β²-homoalanines and found that due to the presence of chiral methyl groups at α-positions, α-ABpeptoids were shown to adopt folding conformations. Here, we report β-ABpeptoids having chiral methyl group at β-positions rather than α-positions as a different class of peptoids with backbone chirality. We developed a facile solid-phase synthetic route that enables the synthesis of β-ABpeptoid oligomers ranging from 2-mer to 8-mer in excellent yields. These oligomers were shown to adopt ordered folding conformations based on circular dichroism (CD) and NMR studies. Overall, these results suggest that β-ABpeptoids represent a novel class of peptidomimetic foldamers that will find a wide range of applications in biomedical and material sciences.