Sequence and Structure of Peptoid Oligomers Can Tune the Photoluminescence of an Embedded Ruthenium Dye

The understanding of structure–function relationships within synthetic biomimetic systems is a fundamental challenge in chemistry. Herein we report the direct correlation between the structure of short peptoid ligands—N-substituted glycine oligomers incorporating 2,2′-bipyridine groups—varied in their monomer sequence, and the photoluminescence of Ru^II centers coordinated by these ligands. Based on circular dichroism and fluorescence spectroscopy we demonstrate that while helical peptoids do not affect the fluorescence of the embedded Ru^II chromophore, unstructured peptoids lead to its significant decay. Transmittance electron microscopy (TEM) revealed significant differences in the arrangements of metal-bound helical versus unstructured peptoids, suggesting that only the latter can have through-space interactions with the ruthenium dye leading to its quenching. High-resolution TEM enabled the remarkable direct imaging of singular ruthenium-bound peptoids and bundles, supporting our explanation for structure-depended quenching. Moreover, this correlation allowed us to fine-tune the luminescence properties of the complexes simply by modifying the sequence of their peptoid ligands. Finally, we also describe the chiral properties of these Ru–peptoids and demonstrate that remote chiral induction from the peptoids backbone to the ruthenium center is only possible when the peptoids are both chiral and helical.     

Stable helical peptoids via covalent side chain to side chain cyclization

Peptoids are oligomeric N-substituted glycines with potential as biologically relevant compounds. Helical peptoids provide an attractive fold for the generation of protein-protein interaction inhibitors. The generation of helical peptoid folds in organic and aqueous media has been limited to strict design rules, as peptoid-folding is mainly directed via the steric direction of alpha-chiral side-chains. Here a new methodology is presented to induce helical folds in peptoids with the aid of side chain to side chain cyclization. Cyclic peptoids were generated via solid-phase synthesis and their folding was studied. The cyclization induces significant helicity in peptoids in organic media, aids the folding in aqueous media, and requires the incorporation of only relatively few chiral aromatic side chains.     

Unique β-Turn Peptoid Structures and Their Application as Asymmetric Catalysts

Peptoids, N-substituted glycine oligomers, represent an important class of peptidomimetics that can fold into three-dimensional structures in solution. Most of the folded peptoid structures, however, resemble helices, and this can limit their applications, specifically in asymmetric catalysis. In this work, for the first time, unique examples of pyrrolidine-based β-turn-like peptoids are described and characterized, both in the solid state, by single-crystal X-ray analysis, and in solution, by circular dichroism spectroscopy. Furthermore, their highly efficient and enantioselective catalytic activity for the production of γ-nitro aldehydes by asymmetric Michael reaction in water was demonstrated. The structural properties and DFT-D3 calculations of the new β-turn-like peptoids, as well as catalytic and spectroscopic studies on designed pyrrolidine-based helical peptoids, suggest that the β-turn structure plays a key role in the stereoselectivity of the catalytic reaction.     

Synthesis of Functionalized Glutamine‐ and Asparagine‐Type Peptoids – Scope and Limitations

N‐Alkylated glycine oligomers (‘peptoids’) can serve as potent peptidomimetic systems. Installing different functional groups can often be a challenge, and minimizes yields and purities. Here, we describe the synthesis of different amide‐containing submonomers which were obtained as free bases, as well as their incorporation into peptoids. By using the free amines, the coupling results on solid support could be improved, and various functionalized peptoids were prepared. Additionally, an interesting dimerization side reaction leading to cross‐linked peptoids was observed during synthesis.     

Expedient synthesis and design strategies for new peptoid construction

[reaction: see text] A range of peptoids can be prepared efficiently using microwave-assisted solid-phase chemistry in a commercial reactor. This method is most effective for the installation of electronically deactivated benzylic amines. The systematic incorporation of these amines into peptoids can deliver oligomers capable of displaying unique and stable structural motifs-microwave-assisted solid-phase synthesis will enable their future study and application.     

Synthesis of biaryl-linked cyclic peptoids

Peptoids, a class of peptidomimetic, have gained considerable attention as potential therapeutic agents due to properties such as biocompatibility and resistance to enzymatic degradation. In linear peptoids, conformational heterogeneity can arise due to cis/trans isomerization around the backbone tertiary amide bond which has led to an increasing interest in cyclic peptoids. Biaryl linkages appear as a common structural motif in many synthetic and naturally occurring cyclic peptides but they are yet to be utilized in the formation of cyclic peptoids. Herein, we describe the application of a solid-phase Suzuki cross-coupling strategy as a means to prepare of a series of biaryl-linked cyclic peptoids. The methodology presented allows access to a range of novel biaryl containing cyclic peptoids with varying ring sizes.     

Synthesis of some cyclic indolic peptoids as potential antibacterials

The synthesis of cyclic peptoids containing an indole hydrophobic scaffold has been realised through the ring-closing metathesis of diallylated precursors. The precursors and their cyclic counterparts possessed poor antibacterial activity in contrast to previously reported cyclic peptoids containing hydrophobic scaffolds.     

Extraordinarily robust polyproline type I peptoid helices generated via the incorporation of α-chiral aromatic N-1-naphthylethyl side chains

Peptoids, or oligomers of N-substituted glycines, are a class of foldamers that have shown extraordinary functional potential since their inception nearly two decades ago. However, the generation of well-defined peptoid secondary structures remains a difficult task. This challenge is due, in part, to the lack of a thorough understanding of peptoid sequence-structure relationships and, consequently, an incomplete understanding of the peptoid folding process. We seek to delineate sequence-structure relationships through the systematic study of noncovalent interactions in peptoids and the design of novel amide side chains capable of such interactions. Herein, we report the synthesis and detailed structural analysis of a series of (S)-N-(1-naphthylethyl)glycine (Ns1npe) peptoid homo-oligomers by X-ray crystallography, NMR spectroscopy, and circular dichroism (CD) spectroscopy. Four of these peptoids were found to adopt well-defined structures in the solid state, with dihedral angles similar to those observed in polyproline type I (PPI) peptide helices and in peptoids with α-chiral side chains. The X-ray crystal structure of a representative Ns1npe tetramer revealed an all cis-amide helix, with approximately three residues per turn, and a helical pitch of approximately 6.0 ?. 2D-NMR analysis of the length-dependent Ns1npe series showed that these peptoids have very high overall backbone amide K(cis/trans) values in acetonitrile, indicative of conformationally homogeneous structures in solution. Additionally, CD spectroscopy studies of the Ns1npe homo-oligomers in acetonitrile and methanol revealed a striking length-dependent increase in ellipticity per amide. These Ns1npe helices represent the most robust peptoid helices to be reported, and the incorporation of (S)-N-(1-naphthylethyl)glycines provides a new approach for the generation of stable helical structure in this important class of foldamers.     

A simple strategy for the construction of combinatorial cyclic peptoid libraries

Here we describe a simple method that allows for rapid and easy sequence determination of cyclic peptoids. The key idea in this strategy is a post-screening "ring-opening" reaction to convert cyclic peptoids selected from a high-throughput screen into linear peptoids, which can be sequenced by tandem mass spectrometry. Thus, there is no need for encoding.     

Design and facile solid-phase synthesis of conformationally constrained bicyclic peptoids

Triazine-bridged bicyclic peptoids as conformationally constrained peptidomimetics are described. Bicyclic peptoids composed of 6-12 peptoid residues (m, n = 3-6) were synthesized in excellent yields using a highly efficient solid-phase synthetic route.     

Microwave-assisted solid-phase synthesis of peptoids

Microwave irradiation reduces the reaction time for the solid-phase synthesis of peptoids. Under these conditions, coupling of each residue requires only 1 min. The purity and yields of peptoids synthesized in this way are as good as or better than those achieved using standard methods. [reaction: see text]     

Peptoids with Antibiofilm Activity against the Gram Negative Obligate Anaerobe,Fusobacterium nucleatum

Peptoids (oligo N-substituted glycines) are peptide analogues, which can be designed to mimic host antimicrobial peptides, with the advantage that they are resistant to proteolytic degradation. Few studies on the antimicrobial efficacy of peptoids have focused on Gram negative anaerobic microbes associated with clinical infections, which are commonly recalcitrant to antibiotic treatment. We therefore studied the cytotoxicity and antibiofilm activity of a family of peptoids against the Gram negative obligate anaerobe Fusobacterium nucleatum, which is associated with infections in the oral cavity. Two peptoids, peptoid 4 (NaeNpheNphe)4 and peptoid 9 (NahNspeNspe)₃ were shown to be efficacious against F. nucleatum biofilms at a concentration of 1 μM. At this concentration, peptoids 4 and 9 were not cytotoxic to human erythrocytes or primary human gingival fibroblast cells. Peptoids 4 and 9 therefore have merit as future therapeutics for the treatment of oral infections.     

Fast and efficient microwave-assisted synthesis of functionalized peptoids via Ugi reactions

A wide range of N-alkylglycines (peptoids) can be efficiently prepared via Ugi reactions using microwave irradiations. The results confirm the versatility and efficiency of the methodology for the preparation of functionalized peptoids. The products can be used in consecutive Ugi reactions to yield cyclic peptoids of potential biological interest.     

Kinetics and equilibria of cis/trans isomerization of backbone amide bonds in peptoids

The biological activities of N-substituted glycine oligomers (peptoids) have been the subject of extensive research. As compared to peptides, both the cis and trans conformations of the backbone amide bonds of peptoids can be significantly populated. Thus, peptoids are mixtures of configurational isomers, with the number of isomers increasing by a factor of 2 with each additional monomer residue. Here we report the results of a study of the kinetics and equilibria of cis/trans isomerization of the amide bonds of N-acetylated peptoid monomers, dipeptoids, and tripeptoids by NMR spectroscopy. Resonance intensities indicate the cis conformation of the backbone amide bonds of the peptoids studied is more populated than is generally the case for the analogous secondary amide bond to proline residues in acyclic peptides. Rate constants were measured by inversion-magnetization transfer techniques over a range of temperatures, and activation parameters were derived from the temperature dependence of the rate constants. The rate of cis/trans isomerization by rotation around the amide bonds in the peptoids studied is generally slower than that around amide bonds to proline residues and takes place on the NMR inversion-magnetization transfer time scale only by rotation around the amide bond to the C-terminal peptoid residue.     

Solution-phase synthesis of aminooxy peptoids in the C to N and N to C directions

[structure: see text] Aminooxy peptoids, which are potential peptidomimetics, were synthesized by a stepwise monomer assembly. Ns-protected N-substituted aminooxyacetate tert-butyl esters were used as a monomer in both the C to N and the N to C directions. Submonomer synthesis of aminooxy peptoids is also described.     

Helical peptoid mimics of magainin-2 amide

A series of peptoid oligomers were designed as helical, cationic, and facially amphipathic mimics of the magainin-2 amide antibacterial peptide. We used circular dichroism spectroscopy to determine the conformation of these peptoids in aqueous buffer and in the presence of bacterial membrane-mimetic lipid vesicles, composed of a 7:3 mol ratio of POPE:POPG. We found that certain peptoids, which displayed characteristically helical CD in buffer and lipid vesicles, exhibit selective (nonhemolytic) and potent antibacterial activity against both Gram-positive and Gram-negative bacteria. In contrast, peptoids that exhibit weak CD, reminiscent of that of a peptide random coil, were ineffective antibiotics. In a manner similar to the natural magainin peptides, we find a correlation between peptoid lipophilicity and hemolytic propensity. We observe that a minimum length of approximately 12 peptoid residues may be required for antibacterial activity. We also see evidence that a helix length between 24 and 34 A may provide optimal antibacterial efficacy. These results provide the first example of a water-soluble, structured, bioactive peptoid.     

Electron Capture Dissociation Studies of the Fragmentation Patterns of Doubly Protonated and Mixed Protonated-Sodiated Peptoids

The fragmentation patterns of a group of doubly protonated ([P + 2H]²⁺) and mixed protonated-sodiated ([P + H + Na]²⁺) peptide-mimicking oligomers, known as peptoids, have been studied using electron capturing dissociation (ECD) tandem mass spectrometry techniques. For all the peptoids studied, the primary backbone fragmentation occurred at the N-C_α bonds. The N-terminal fragment ions, the C-ions (protonated) and the C′-ions (sodiated) were observed universally for all the peptoids regardless of the types of charge carrier. The C-terminal ions varied depending on the type of charge carrier. The doubly protonated peptoids with at least one basic residue located at a position other than the N-terminus fragmented by producing the Z^?-series of ions. In addition, most doubly protonated peptoids also produced the Y-series of ions with notable abundances. The mixed protonated-sodiated peptoids fragmented by yielding the Z^?′-series of ions in addition to the C′-series. Chelation between the sodium cation and the amide groups of the peptoid chain might be an important factor that could stabilize both the N-terminal and the C-terminal fragment ions. Regardless of the types of the charge carrier, one notable fragmentation for all the peptoids was the elimination of a benzylic radical from the odd-electron positive ions of the protonated peptoids ([P + 2H]^?+) and the sodiated peptoids ([P + H + Na]^?+). The study showed potential utility of using the ECD technique for sequencing of peptoid libraries generated by combinatorial chemistry.

Synthesis of carbazole-linked cyclic and acyclic peptoids with antibacterial activity

This paper describes the synthesis of several novel cyclic and acyclic peptoids, the former structurally comprising a tripeptide moiety linked through a carbazole scaffold. In a key step, a ring-closing metathesis reaction was used giving efficient access to this new class of cyclic peptoids. The target compounds were tested against Staphylococcus aureus (ATCC 6538P) and their minimum inhibitory concentration (MIC) values were determined. These compounds showed moderate to poor activities with MIC values ranging from 15-250 μg/mL.     

One pot synthesis of selenocysteine containing peptoid libraries by Ugi multicomponent reactions in water

Selenocysteine containing peptoids and peptide-peptoid conjugates were synthesized by combinatorial Ugi-MCRs (multicomponent reactions) in water: for the first time, an acetal (selenoacetal 2a) was used in Ugi-MCR to furnish selenocysteine peptoids in one step as model compounds for selenocysteine peptides and proteins.     

Probing the structural requirements of peptoids that inhibit HDM2-p53 interactions

Many cellular processes are controlled by protein-protein interactions, and selective inhibition of these interactions could lead to the development of new therapies for several diseases. In the area of cancer, overexpression of the protein, human double minute 2 (HDM2), which binds to and inactivates the protein p53, has been linked to tumor aggressiveness and drug resistance. In general, inhibition of protein-protein interactions with synthetic molecules is challenging and currently remains a largely uncharted area for drug development. One strategy to create inhibitors of protein-protein interactions is to recreate the three-dimensional arrangement of side chains that are involved in the binding of one protein to another, using a nonnatural scaffold as the attachment point for the side chains. In this study, we used oligomeric peptoids as the scaffold to begin to develop a general strategy in which we could rationally design synthetic molecules that can be optimized for inhibition of protein-protein interactions. Structural information on the HDM2-p53 complex was used to design our first class of peptoid inhibitors, and we provide here, in detail, the strategy to modify peptoids with the appropriate side chains that are effective inhibitors of HDM2-p53 binding. While we initially tried to develop rigid, helical peptoids as HDM2 binders, the best inhibitors were surprisingly peptoids that lacked any helix-promoting groups. These results indicate that starting with rigid peptoid scaffolds may not always be optimal to develop new inhibitors.