Structure-function relationships in peptoids: recent advances toward deciphering the structural requirements for biological function

Self-Assembling and Pore-Forming Peptoids as Antimicrobial Biomaterials

Bacterial infections have been a serious threat to mankind throughout history. Natural antimicrobial peptides (AMPs) and their membrane disruption mechanism have generated immense interest in the design and development of synthetic mimetics that could overcome the intrinsic drawbacks of AMPs, such as their susceptibility to proteolytic degradation and low bioavailability. Herein, by exploiting the self-assembly and pore-forming capabilities of sequence-defined peptoids, we discovered a family of low-molecular weight peptoid antibiotics that exhibit excellent broad-spectrum activity and high selectivity toward a panel of clinically significant Gram-positive and Gram-negative bacterial strains, including vancomycin-resistant Enterococcus faecalis (VREF), methicillin-resistant Staphylococcus aureus (MRSA), methicillin-resistant Staphylococcus epidermidis (MRSE), Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Tuning the peptoid side chain chemistry and structure enabled us to tune the efficacy of antimicrobial activity. Mechanistic studies using transmission electron microscopy (TEM), bacterial membrane depolarization and lysis, and time-kill kinetics assays along with molecular dynamics simulations reveal that these peptoids kill both Gram-positive and Gram-negative bacteria through a membrane disruption mechanism. These robust and biocompatible peptoid-based antibiotics can provide a valuable tool for combating emerging drug resistance.

Functionalized Surface Coatings for Rigid Contact Lenses

This research evolves into a comparative study of three different phenolic composites as coatings for rigid contact lenses, with a particular emphasis on enhancing their antifouling properties and hydrophobicity. The primary layer, comprised of diverse phenolic compounds, serves as a sturdy foundation. An exclusive secondary layer, featuring synthetic peptoids, is introduced to further minimize biofouling. Validated through X-ray photoelectron spectroscopy, the surface analysis confirms the successful integration of the polyphenolic layers and the subsequent grafting of peptoids onto the lens surface. The efficacy of the proposed coatings is substantiated through protein adsorption tests, providing definitive evidence of their antifouling capabilities. This research employs a nuanced assessment of coating performance, utilizing the quantification of fluorescence intensity to gauge effectiveness. Additionally, contact angle measurements offer insights into wettability and surface characteristics, contributing to a comprehensive understanding of the coating's practicality.

Innovative peptide architectures: advancements in foldamers and stapled peptides for drug discovery

INTRODUCTION

Peptide foldamers play a critical role in pharmaceutical research and biomedical applications. This review highlights recent (post-2020) advancements in novel foldamers, synthetic techniques, and their applications in pharmaceutical research.

AREAS COVERED

The authors summarize the structures and applications of peptide foldamers such as α, β, γ-peptides, hydrocarbon-stapled peptides, urea-type foldamers, sulfonic-γ-amino acid foldamers, aromatic foldamers, and peptoids, which tackle the challenges of traditional peptide drugs. Regarding antimicrobial use, foldamers have shown progress in their potential against drug-resistant bacteria. In drug development, peptide foldamers have been used as drug delivery systems (DDS) and protein-protein interaction (PPI) inhibitors.

EXPERT OPINION

These structures exhibit resistance to enzymatic degradation, are promising for therapeutic delivery, and disrupt crucial PPIs associated with diseases such as cancer with specificity, versatility, and stability, which are useful therapeutic properties. However, the complexity and cost of their synthesis, along with the necessity for thorough safety and efficacy assessments, necessitate extensive research and cross-sector collaboration. Advances in synthesis methods, computational modeling, and targeted delivery systems are essential for fully realizing the therapeutic potential of foldamers and integrating them into mainstream medical treatments.

Using Enhanced Sampling Simulations to Study the Conformational Space of Chiral Aromatic Peptoid Monomers

Peptoids, or N-substituted glycines, are peptide-like materials that form a wide variety of secondary structures owing to their enhanced flexibility and a diverse collection of possible side chains. Compared to that of peptides, peptoids have a substantially more complex conformational landscape. This is mainly due to the ability of the peptoid amide bond to exist in both cis- and trans-conformations. This makes conventional molecular dynamics simulations and even some enhanced sampling approaches unable to sample the complete energy landscapes. In this article, we present an extension to the CGenFF-NTOID peptoid atomistic forcefield by adding parameters for four side chains to the previously available collection. We employ explicit solvent well-tempered metadynamics simulations to optimize our forcefield parameters and parallel bias metadynamics to study the cis-trans isomerism for SN1-phenylethyl (s1pe) and SN1-naphthylethyl (s1ne) peptoid monomers, the free energy minima generated from which are validated with available experimental data. In the absence of experimental data, we supported our atomistic simulations with ab initio calculations. This work represents an important step toward the computational design of peptoid-based materials.

Synthetically encoded complementary oligomers

Creating the next generation of advanced materials will require controlling molecular architecture to a degree typically achieved only in biopolymers. Sequence-defined polymers take inspiration from biology by using chain length and monomer sequence as handles for tuning structure and function. These sequence-defined polymers can assemble into discrete structures, such as molecular duplexes, via reversible interactions between functional groups. Selectivity can be attained by tuning the monomer sequence, thereby creating the need for chemical platforms that can produce sequence-defined polymers at scale. Developing sequence-defined polymers that are specific for their complementary sequence and achieve their desired binding strengths is critical for producing increasingly complex structures for new functional materials. In this Review Article, we discuss synthetic platforms that produce sequence-defined, duplex-forming oligomers of varying length, strength and association mode, and highlight several analytical techniques used to characterize their hybridization.

Ugi efficient synthesis of novel N-alkylated lipopeptides, antimicrobial properties and computational studies in Staphylococcus aureus via MurD antibacterial target

Lipopeptides are medicinally essential building blocks with strong hemolytic, antifungal and antibiotic potential. In the present research article, we are presenting our findings regarding the synthesis of N-alkylated lipopeptides via Ugi four-component approach, their antimicrobial potential against pathogenic (Gram-positive and Gram-negative) bacteria, as well as computational studies to investigate the compounds binding affinity and dynamic behavior with MurD antibacterial target. Molecular docking demonstrated the compounds have good binding ability with MurD enzyme. The FT94, FT95 and FT97 compounds revealed binding affinity scores of -8.585 kcal mol- 1, -7.660 kcal mol- 1 and -7.351 kcal mol- 1, respectively. Furthermore, dynamics analysis pointed the systems high structure dynamics. The docking and simulation results were validated by binding free energies, demonstrating solid intermolecular interactions and in the assay in vitro, the Minimal Inhibitory Concentration (MIC) of FT97 to Staphylococcus aureus (S. aureus) was 62.5 μg/mL. In conclusion, a moderate inhibitory response of peptoid FT97 was observed against the Gram-positive bacteria, S. aureus and B. cereus.

Origins of Conformational Heterogeneity in Peptoid Helices Formed by Chiral N-1-Phenylethyl Sidechains

N-substituted glycines (polypeptoids) containing chiral hydrophobic sidechains are known to fold into biomimetic alpha helices. These helix formers often produce conformationally heterogeneous structures and are difficult to characterize at a sub-nanometer resolution. Previously, peptoid N-1-phenylethyl (R)-enantiomer sidechains (Nspe) were inferred from various experiments to form right-handed helices and (S)-enantiomers (Nrpe), left-handed helices. Prior computational work for N(s/r)pe oligomers has struggled to reproduce this trend. Herein, quantum mechanics calculations and molecular dynamics simulations are used to understand the origins of this discrepancy. Results from DFT and molecular mechanics calculations on a variety of Nspe and Nrpe oligomers as a function of chain length are in agreement, showing that Nspe and Nrpe prefer left- and right-handed helices, respectively. Additional metadynamics simulations are used to study Nrpe and Nspe oligomers folding in water. These results show that the free-energy driving forces for assembly into a helical backbone configuration are very small (within ∼k_BT). Lastly, we compare DFT calculations for other experimentally characterized peptoid sidechains, N(r/s)sb, N(r/s)tbe, and N(r/s)npe. In this analysis, we show that peptoid sidechains determined to be more robust experimentally (tbe and npe) have helical preferences opposite the trend seen in less robust assemblies formed by N(r/s)pe and N(r/s)sb chemistries. The more robust tbe and nnpe favor the (S)-enantiomer to right-handed and the (R)-enantiomers to left-handed helices.

A Review on the Synthesis of Polypeptoids

Polyeptoids are a promising class of polypeptide mimetic biopolymers based on N-substituted glycine backbones. Because of the high designability of their side chains, polypeptoids have a wide range of applications in surface antifouling, biosensing, drug delivery, and stimuli-responsive materials. To better control the structures and properties of polypeptoids, it is necessary to understand different methods for polypeptoid synthesis. This review paper summarized and discussed the main synthesis methods of polypeptoids: the solid-phase submonomer synthesis method, ring-opening polymerization method and Ugi reaction method.

Crosslinker structure modulates bulk mechanical properties and dictates hMSC behavior on hyaluronic acid hydrogels

Synthetic hydrogels are attractive platforms due in part to their highly tunable mechanics, which impact cell behavior and secretory profile. These mechanics are often controlled by altering the number of crosslinks or the total polymer concentration in the gel, leading to structure-property relationships that inherently couple network connectivity to the overall modulus. In contrast, the native extracellular matrix (ECM) contains structured biopolymers that enable stiff gels even at low polymer content, facilitating 3D cell culture and permeability of soluble factors. To mimic the hierarchical order of natural ECM, this work describes a synthetic hydrogel system in which mechanics are tuned using the structure of sequence-defined peptoid crosslinkers, while fixing network connectivity. Peptoid crosslinkers with different secondary structures are investigated: 1) a helical, molecularly stiff peptoid, 2) a non-helical, less stiff peptoid, and 3) an unstructured, relatively flexible peptoid. Bulk hydrogel storage modulus increases when crosslinkers of higher chain stiffness are used. In-vitro studies assess the viability, proliferation, cell morphology, and immunomodulatory activity of human mesenchymal stem cells (hMSCs) on each hydrogel substrate. Matrix mechanics regulate the morphology of hMSCs on the developed substrates, and all of the hydrogels studied upregulate IDO production over culture on TCP. Softer substrates further this upregulation to a plateau. Overall, this system offers a biomimetic strategy for decoupling hydrogel storage modulus from network connectivity, enabling systematic study of biomaterial properties on hMSC behavior and enhancement of cellular functionality for therapeutic applications. STATEMENT OF SIGNIFICANCE: Various strategies to tune hydrogel mechanics have been developed to control human mesenchymal stem cell (hMSC) behavior and regulate their immunomodulatory potential. However, these strategies typically couple mechanics to network connectivity, which in turn changes other hydrogel properties such as permeability that may have unintended effects on hMSC behavior. This work presents a strategy to tune hydrogel mechanics using crosslinkers with different secondary structure and molecular rigidity. This strategy successfully decouples hydrogel moduli from crosslinker stoichiometry and mimics the hierarchical nature of the native extracellular matrix. The moduli of the developed hydrogels led to significant impacts on hMSC morphology and proliferation, and increased immunomodulatory potential, indicating that molecular rigidity is a promising avenue to control engineered ECM mechanics for therapeutic applications.

Fluorescent Peptomer Substrates for Differential Degradation by Metalloproteases

Proteases, especially MMPs, are attractive biomarkers given their central role in both physiological and pathological processes. Distinguishing MMP activity with degradable substrates, however, is a difficult task due to overlapping substrate specificity profiles. Here, we developed a system of peptomers (peptide-peptoid hybrids) to probe the impact of non-natural residues on MMP specificity for an MMP peptide consensus sequence. Peptoids are non-natural, N-substituted glycines with a large side-chain diversity. Given the presence of a hallmark proline residue in the P3 position of MMP consensus sequences, we hypothesized that peptoids may offer N-substituted alternatives to generate differential interactions with MMPs. To investigate this hypothesis, peptomer substrates were exposed to five different MMPs, as well as bacterial collagenase, and monitored by fluorescence resonance energy transfer and liquid chromatography-mass spectrometry to determine the rate of cleavage and the composition of degraded fragments, respectively. We found that peptoid residues are well tolerated in the P3 and P3' substrate sites and that the identity of the peptoid in these sites displays a moderate influence on the rate of cleavage. However, peptoid residues were even better tolerated in the P1 substrate site where activity was more strongly correlated with side-chain identity than side-chain position. All MMPs explored demonstrated similar trends in specificity for the peptomers but exhibited different degrees of variability in proteolytic rate. These kinetic profiles served as "fingerprints" for the proteases and yielded separation by multivariate data analysis. To further demonstrate the practical application of this tunability in degradation kinetics, peptomer substrates were tethered into hydrogels and released over distinct timescales. Overall, this work represents a significant step toward the design of probes that maximize differential MMP behavior and presents design rules to tune degradation kinetics with peptoid substitutions, which has promising implications for diagnostic and prognostic applications using array-based sensors.

Unveiling the conformational landscape of achiral all-cis tert-butyl β-peptoids

The synthesis and conformational study of N-substituted β-alanines with tert-butyl side chains is described. The oligomers prepared by submonomer synthesis and block coupling methods are up to 15 residues long and are characterised by amide bonds in the cis-conformation. A conformational study comprising experimental solution NMR spectroscopy, X-ray crystallography and molecular modeling shows that despite their intrinsic higher conformational flexibility compared to their α-peptoid counterparts, this family of achiral oligomers adopt preferred secondary structures including a helical conformation close to that described with (1-naphthyl)ethyl side chains but also a novel ribbon-like conformation.

A Field Guide to Optimizing Peptoid Synthesis

N-Substituted glycines (peptoids) are a class of peptidomimetic molecules used as materials for health, environmental, and drug delivery applications. Automated solid-phase synthesis is the most widely used approach for preparing polypeptoids, with a range of published protocols and modifications for selected synthetic targets. Simultaneously, emerging solution-phase syntheses are being leveraged to overcome limitations in solid-phase synthesis and access high-molecular weight polypeptoids. This Perspective aims to outline strategies for the optimization of both solid- and solution-phase synthesis, provide technical considerations for robotic synthesizers, and offer an outlook on advances in synthetic methodologies. The solid-phase synthesis sections explore steps for protocol optimization, accessing complex side chains, and adaptation to robotic synthesizers; the sections on solution-phase synthesis cover the selection of initiators, side chain compatibility, and strategies for controlling polymerization efficiency and scale. This text acts as a "field guide" for researchers aiming to leverage the flexibility and adaptability of peptoids in their research.

Aligned peptoid-based macrodiscs for structural studies of membrane proteins by oriented-sample NMR

Development of a robust, uniform, and magnetically orientable lipid mimetic will undoubtedly advance solid-state NMR of macroscopically aligned membrane proteins. Here, we report on a novel lipid membrane mimetic based on peptoid belts. The peptoids, composed of 15 residues, were synthesized by alternating N-(2-phenethyl)glycine with N-(2-carboxyethyl)glycine residues at a 2:1 molar ratio. The chemically synthesized peptoids possess a much lower degree of polydispersity versus styrene-maleic acid polymers, thus yielding uniform discs. Moreover, the peptoid oligomers are more flexible and do not require a specific folding, unlike lipoproteins, in order to wrap around the hydrophobic membrane core. The NMR spectra measured for the membrane-bound form of Pf1 coat protein incorporated in this new lipid mimetics demonstrate a higher order parameter and uniform linewidths compared with the conventional bicelles and peptide-based macrodiscs. Importantly, unlike bicelles, the peptoid-based macrodiscs are detergent free.

Synthesis and Studies of Bulky Cycloalkyl α,β-Dehydroamino Acids that Enhance Proteolytic Stability

Three new bulky cycloalkyl α,β-dehydroamino acids (ΔAAs) have been designed and synthesized. Each residue enhances the rigidity of model peptides and their stability to proteolysis, with larger ring sizes exhibiting greater effects. Peptides containing bulky cycloalkyl ΔAAs are inert to conjugate addition by a nucleophilic thiol. The results suggest that these residues will be effective tools for improving the proteolytic stability of bioactive peptides.

Strategies to Control the cis-trans Isomerization of Peptoid Amide Bonds

Peptoids are oligomers of N-substituted glycine units. They structurally resemble peptides but, unlike natural peptides, the side chains of peptoids are present on the amide nitrogen atoms instead of the α-carbons. The N-substitution improves cell-permeability of peptoids and enhance their proteolytic stability over natural peptides. Therefore, peptoids are ideal peptidomimetic candidates for drug discovery, especially for intracellular targets. Unfortunately, most peptoid ligands discovered so far possess moderate affinity towards their biological targets. The moderate affinity of peptoids for biomacromolecules is linked to their conformational flexibility, which causes substantial entropic loss during the peptoid-biomacromolecule binding process. The conformational flexibility of peptoids is caused by the lack of backbone chirality, absence of hydrogen bond donors (NH) in their backbone to form CO···HN hydrogen bonds and the facile cis-trans isomerization of their tertiary amide bonds. In recent years, many investigators have shown that the incorporation of specific side chains with unique steric and stereoelectronic features can favourably shift the cis-trans equilibria of peptoids towards one of the two isomeric forms. Such strategies are helpful to design homogenous peptoid oligomers having well defined secondary structures. Herein, we discuss the strategies developed over the years to control the cis-trans isomerization of peptoid amide bonds.

Unbiased peptoid cell screen identifies a peptoid targeting newly appeared cell surface vimentin on tumor transformed early lung cancer cells

To identify potential new reagents and biomarkers for early lung cancer detection we combined the use of a novel preclinical isogenic model of human lung epithelial cells comparing non-malignant cells with those transformed to full malignancy using defined oncogenic changes and our on-bead two color (red and green stained cells) (OBTC) peptoid combinatorial screening methodology. The preclinical model used normal parent lung epithelial cells (HBEC3-KT, labeled with green dye) and isogenic fully malignant transformed derivatives (labeled with a red dye) via the sequential introduction of key genetic alterations of p53 knockdown, oncogenic KRAS and overexpression of cMYC (HBEC3^{p53, KRAS, cMYC}). Using the unbiased OBTC screening approach, we tested 100,000 different peptoids and identified only one (named JM3A) that bound to the surface of the HBEC3^{p53, KRAS, cMYC} cells (red cells) but not HBEC3-KT cells (green cells). Using the JM3A peptoid and proteomics, we identified the protein bound as vimentin using multiple validation approaches. These all confirmed the cell surface expression of vimentin (CSV) on transformed (HBEC3^{p53, KRAS, cMYC}) but not on untransformed (HBEC3-KT) cells. JM3A coupled with fluorophores was able to detect and stain cell surface vimentin on very early stage lung cancers but not normal lung epithelial cells in a fashion comparable to that using anti-vimentin antibodies. We conclude: using a combined isogenic preclinical model of lung cancer and two color screening of a large peptoid library, we have identified differential expression of cell surface vimentin (CSV) after malignant transformation of lung epithelial cells, and developed a new peptoid reagent (JM3A) for detection of CSV which works well in staining of early stage NSCLCs. This new, highly specific, easy to prepare, CSV detecting JM3A peptoid provides an important new reagent for identifying cancer cells in early stage tumors as well as a resource for detection and isolating of CSV expressing circulating tumor cells.

Bottlebrush polymers with flexible enantiomeric side chains display differential biological properties

Chirality and molecular conformation are central components of life: biological systems rely on stereospecific interactions between discrete (macro)molecular conformers, and the impacts of stereochemistry and rigidity on the properties of small molecules and biomacromolecules have been intensively studied. Nevertheless, how these features affect the properties of synthetic macromolecules has received comparably little attention. Here we leverage iterative exponential growth and ring-opening metathesis polymerization to produce water-soluble, chiral bottlebrush polymers (CBPs) from two enantiomeric pairs of macromonomers of differing rigidity. Remarkably, CBPs with conformationally flexible, mirror image side chains show several-fold differences in cytotoxicity, cell uptake, blood pharmacokinetics and liver clearance; CBPs with comparably rigid, mirror image side chains show no differences. These observations are rationalized with a simple model that correlates greater conformational freedom with enhanced chiral recognition. Altogether, this work provides routes to the synthesis of chiral nanostructured polymers and suggests key roles for stereochemistry and conformational rigidity in the design of future biomaterials.

Bio-instructive materials on-demand - combinatorial chemistry of peptoids, foldamers, and beyond

Combinatorial chemistry allows for the rapid synthesis of large compound libraries for high throughput screenings in biology, medicinal chemistry, or materials science. Especially compounds from a highly modular design are interesting for the proper investigation of structure-to-activity relationships. Permutations of building blocks result in many similar but unique compounds. The influence of certain structural features on the entire structure can then be monitored and serve as a starting point for the rational design of potent molecules for various applications. Peptoids, a highly diverse class of bioinspired oligomers, suit perfectly for combinatorial chemistry. Their straightforward synthesis on a solid support using repetitive reaction steps ensures easy handling and high throughput. Applying this modular approach, peptoids are readily accessible, and their interchangeable side-chains allow for various structures. Thus, peptoids can easily be tuned in their solubility, their spatial structure, and, consequently, their applicability in various fields of research. Since their discovery, peptoids have been applied as antimicrobial agents, artificial membranes, molecular transporters, and much more. Studying their three-dimensional structure, various foldamers with fascinating, unique properties were discovered. This non-comprehensive review will state the most interesting discoveries made over the past years and arouse curiosity about what may come.

A novel peptidomimetic therapeutic for selective suppression of lung cancer stem cells over non-stem cancer cells

Cancers are highly heterogeneous and typically contain a small subset of drug-resisting cells called tumor initiating cells or cancer stem cells (CSCs). CSCs can self-renew, divide asymmetrically, and often cause tumor invasion and metastasis. Therefore, treatments specifically targeting CSCs are critical to improve patient survival. Recently, we identified a highly specific peptidomimetic (peptoid - PCS2) that selectively binds to the CSC subpopulation of lung cancer over the remaining cancer cells (non-CSCs). Subsequently, we identified plectin as the target of PCS2. Plectin is an intracellular structural protein, which is involved in tumor invasion and metastasis when it appears on cell surface. While PCS2 monomer did not display any anti-cancer activity, we designed a series of homo-dimeric versions of PCS2, and identified PCS2D1.2 optimized homo-dimer that displayed highly specific cytotoxicity towards CSCs over non-CSCs. PCS2D1.2 effectively blocked the in vitro colony formation and cell migration, hallmarks of CSCs. Furthermore, PCS2D1.2 reduced the in vivo tumor formation. In both in vitro and in vivo studies, PCS2D1.2 effectively reduced plectin expression and/or plectin-rich CSCs, but had no effect on non-CSCs. Therefore, PCS2D1.2 has the potential to be developed as a highly CSC specific drug candidate, which can be used in combination with current anti-cancer drugs.

"Molecular Masks" for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry

Coronavirus Disease 2019 (COVID-19) remains a global health crisis, despite the development and success of vaccines in certain countries. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, uses its spike protein to bind to the human cell surface receptor angiotensin-converting enzyme 2 (ACE2), which allows the virus to enter the human body. Using our unique cell screening technology, we identified two ACE2-binding peptoid compounds and developed dimeric derivatives (ACE2P1D1 and ACE2P2D1) that effectively blocked spike protein-ACE2 interaction, resulting in the inhibition of SARS-CoV-2 pseudovirus entry into human cells. ACE2P1D1 and ACE2P2D1 also blocked infection by a D614G mutant pseudovirus. More importantly, these compounds do not decrease ACE2 expression nor its enzyme activity (which is important in normal blood pressure regulation), suggesting safe applicability in humans

Helical Peptoid Ions in the Gas Phase: Thwarting the Charge Solvation Effect by H-Bond Compensation

Folding and unfolding processes are key aspects that should be mastered for the design of foldamer molecules for targeted applications. In contrast to the solution phase, in vacuo conditions represent a well-defined environment to analyze the intramolecular interactions that largely control the folding/unfolding dynamics. Ion mobility mass spectrometry coupled to theoretical modeling represents an efficient method to decipher the spatial structures of gaseous ions, including foldamers. However, charge solvation typically compacts the ion structure in the absence of strong stabilizing secondary interactions. This is the case in peptoids that are synthetic peptide regioisomers whose side chains are connected to the nitrogen atoms of the backbone instead of α-carbon as in peptides, thus implying the absence of H-bonds among the core units of the backbone. A recent work indeed reported that helical peptoids based on Nspe units formed in solution do not retain their secondary structure when transferred to the gas phase upon electrospray ionization (ESI). In this context, we demonstrate here that the helical structure of peptoids bearing (S)-N-(1-carboxy-2-phenylethyl) bulky side chains (Nscp) is largely preserved in the gas phase by the creation of a hydrogen bond network, induced by the presence of carboxylic moieties, that compensates for the charge solvation process.

Towards a streamlined synthesis of peptides containing α,β-dehydroamino acids

Investigation of a strategy to streamline the synthesis of peptides containing α,β-dehydroamino acids (ΔAAs) is reported. The key step involves generating the alkene moiety via elimination of a suitable precursor after it has been inserted into a peptide chain. This process obviates the need to prepare ΔAA-containing azlactone dipeptides to facilitate coupling of these residues. Z-dehydroaminobutyric acid (Z-ΔAbu) could be constructed most efficiently via EDC/CuCl-mediated dehydration of Thr. Formation of Z-ΔPhe by this or other dehydration methods was unsuccessful. Production of the bulky ΔVal residue could be accomplished by DAST-promoted dehydrations of β-OHVal or by DBU-triggered eliminations of sulfonium ions derived from penicillamine derivatives. However, competitive formation of an oxazoline byproduct remains problematic.

Massively Parallel Optimization of the Linker Domain in Small Molecule Dimers Targeting a Toxic r(CUG) Repeat Expansion

RNA contributes to disease pathobiology and is an important therapeutic target. The downstream biology of disease-causing RNAs can be short-circuited with small molecules that recognize structured regions. The discovery and optimization of small molecules interacting with RNA is, however, challenging. Herein, we demonstrate a massively parallel one-bead-one-compound methodology, employed to optimize the linker region of a dimeric compound that binds the toxic r(CUG) repeat expansion [r(CUG)exp] causative of myotonic dystrophy type 1 (DM1). Indeed, affinity selection on a 331,776-member library allowed the discovery of a compound with enhanced potency both in vitro (10-fold) and in DM1-patient-derived myotubes (5-fold). Molecular dynamics simulations revealed additional interactions between the optimized linker and the RNA, resulting in ca. 10 kcal/mol lower binding free energy. The compound was conjugated to a cleavage module, which directly cleaved the transcript harboring the r(CUG)exp and alleviated disease-associated defects.

Peptoids as a Chiral Stationary Phase for Liquid Chromatography: Insights from Molecular Dynamics Simulations

Peptoids are peptide regioisomers with attractive structural tunability in terms of sequence and three-dimensional arrangement. Peptoids are foreseen to have a great potential for many diverse applications, including their utilization as a chiral stationary phase in chromatography. To achieve chiral recognition, a chiral side chain is required to allow specific interactions with a given enantiomer from a racemic mixture. One of the most studied chiral stationary phases, built with (S)-N-1-phenylethyl (Nspe) units, was shown to be successful in resolving racemic mixtures of binaphthyl derivatives. However, there is currently no description at the atomic scale of the factors favoring its enantioselectivity. Here, we take advantage of steered molecular dynamics simulations to mimic the elution process at the atomic scale and present evidence that the predominantly right-handed helical conformation of Nspe peptoids and their ability to form stronger hydrogen bonds with the (S) enantiomer are responsible for the chiral recognition of the popular chiral probe 2,2'-bihydroxy-1,1'-binaphthyl.

N-Arylated peptide: troponyl residue influences the structure and conformation of N-troponylated-(di/tri)-peptides

N-arylated peptides as peptoids influence the structural and conformational changes of small peptides that lead to unique foldamers, even in di-/tri-peptides.

Synthesis and characterization of new Na+ complexes of N-benzyl cyclic peptoids and their role in the ring opening polymerization of l-lactide

Na⁺ complexes of cyclic peptoid were employed for the first time as catalyst for the l-lactide polymerization.

Dimension control on self-assembly of a crystalline core-forming polypeptoid block copolymer: 1D nanofibers versus 2D nanosheets

The balance between the crystallization and solubility of the block copolymer dominates the nanostructures.

Ugi Reaction of Amino Acids: From Facile Synthesis of Polypeptoids to Sequence-Defined Macromolecules

Polypeptoids have been prepared and researched for more than 20 years. However, the efficient generation of polypeptoids and sequence-defined polypeptoids faces many challenges and difficulties. The Ugi reaction of amino acids has recently been introduced into polypeptoid chemistry as a new and powerful method to furnish polypeptoids. In the following mini review, the recent progress on the application of the Ugi reaction of amino acids in polypeptoid science, including polypeptoid from sustainable furfural, sequence-defined polypeptoids, and more is summarized. Moreover, the future development of the Ugi reaction of amino acids in polypeptoid science is discussed.

Structure-Property Relationship Study of N-(Hydroxy)Peptides for the Design of Self-Assembled Parallel β-Sheets

The design of novel and functional biomimetic foldamers remains a major challenge in creating mimics of native protein structures. Herein, we report the stabilization of a remarkably short β-sheet by incorporating N-(hydroxy)glycine (Hyg) residues into the backbone of peptides. These peptide-peptoid hybrids form unique parallel β-sheet structures by self-assembly upon hydrogenation. Our spectroscopic and crystallographic data suggest that the local conformational perturbations induced by N-(hydroxy)amides are outweighed by a network of strong interstrand hydrogen bonds.

Peptide science: A "rule model" for new generations of peptidomimetics

Peptides have been heavily investigated for their biocompatible and bioactive properties. Though a wide array of functionalities can be introduced by varying the amino acid sequence or by structural constraints, properties such as proteolytic stability, catalytic activity, and phase behavior in solution are difficult or impossible to impart upon naturally occurring α-L-peptides. To this end, sequence-controlled peptidomimetics exhibit new folds, morphologies, and chemical modifications that create new structures and functions. The study of these new classes of polymers, especially α-peptoids, has been highly influenced by the analysis, computational, and design techniques developed for peptides. This review examines techniques to determine primary, secondary, and tertiary structure of peptides, and how they have been adapted to investigate peptoid structure. Computational models developed for peptides have been modified to predict the morphologies of peptoids and have increased in accuracy in recent years. The combination of in vitro and in silico techniques have led to secondary and tertiary structure design principles that mirror those for peptides. We then examine several important developments in peptoid applications inspired by peptides such as pharmaceuticals, catalysis, and protein-binding. A brief survey of alternative backbone structures and research investigating these peptidomimetics shows how the advancement of peptide and peptoid science has influenced the growth of numerous fields of study. As peptide, peptoid, and other peptidomimetic studies continue to advance, we will expect to see higher throughput structural analyses, greater computational accuracy and functionality, and wider application space that can improve human health, solve environmental challenges, and meet industrial needs. STATEMENT OF SIGNIFICANCE: Many historical, chemical, and functional relations draw a thread connecting peptides to their recent cognates, the "peptidomimetics". This review presents a comprehensive survey of this field by highlighting the width and relevance of these familial connections. In the first section, we examine the experimental and computational techniques originally developed for peptides and their morphing into a broader analytical and predictive toolbox. The second section presents an excursus of the structures and properties of prominent peptidomimetics, and how the expansion of the chemical and structural diversity has returned new exciting properties. The third section presents an overview of technological applications and new families of peptidomimetics. As the field grows, new compounds emerge with clear potential in medicine and advanced manufacturing.

Impact of Dehydroamino Acids on the Structure and Stability of Incipient 310-Helical Peptides

A comparative study of the impact of small, medium-sized, and bulky α,β-dehydroamino acids (ΔAAs) on the structure and stability of Balaram's incipient 3₁₀-helical peptide (1) is reported. Replacement of the N-terminal Aib residue of 1 with a ΔAA afforded peptides 2a-c that maintained the 3₁₀-helical shape of 1. In contrast, installation of a ΔAA in place of Aib-3 yielded peptides 3a-c that preferred a β-sheet-like conformation. The impact of the ΔAA on peptide structure was independent of size, with small (ΔAla), medium-sized (Z-ΔAbu), and bulky (ΔVal) ΔAAs exerting similar effects. The proteolytic stabilities of 1 and its analogs were determined by incubation with Pronase. Z-ΔAbu and ΔVal increased the resistance of peptides to proteolysis when incorporated at the 3-position and had negligible impact on stability when placed at the 1-position, whereas ΔAla-containing peptides degraded rapidly regardless of position. Exposure of peptides 2a-c and 3a-c to the reactive thiol cysteamine revealed that ΔAla-containing peptides underwent conjugate addition at room temperature, while Z-ΔAbu- and ΔVal-containing peptides were inert even at elevated temperatures. These results suggest that both bulky and more accessible medium-sized ΔAAs should be valuable tools for bestowing rigidity and proteolytic stability on bioactive peptides.

Solid-Phase Insertion of N-mercaptoalkylglycine Residues into Peptides

N-mercaptoalkylglycine residues were inserted into peptides by reacting N-free amino groups of peptides, which were initially synthesized on 2-chlorotrityl resin (Cltr) using the Fmoc/^tBu method, with bromoacetic acid and subsequent nucleophilic replacement of the bromide by reacting with S-4-methoxytrityl- (Mmt)/S-trityl- (Trt) protected aminothiols. The synthesized thiols containing peptide–peptoid hybrids were cleaved from the resin, either protected by treatment with dichloromethane (DCM)/trifluoroethanol (TFE)/acetic acid (AcOH) (7:2:1), or deprotected (fully or partially) by treatment with trifluoroacetic acid (TFA) solution using triethylsilane (TES) as a scavenger.

Reverse Turn and Loop Secondary Structures in Stereodefined Cyclic Peptoid Scaffolds

Controlling the network of intramolecular interactions encoded by Nα-chiral side chains and the equilibria between cis- and trans-amide junctions in cyclic peptoid architectures constitutes a significant challenge for the construction of stable reverse turn and loop structures. In this contribution, we reveal, with the support of NMR spectroscopy, single-crystal X-ray crystallography and density functional theory calculations, the relevant noncovalent interactions stabilizing tri-, tetra-, hexa-, and octameric cyclic peptoids (as free hosts and host-guest complexes) with strategically positioned N-(S)-(1-phenylethyl)/N-benzyl side chains, and how these interactions influence the backbone topological order. With the help of theoretical models and spectroscopic/diffractometric studies, we disclose new γ-/β-turn and loop structures present in α-peptoid-based macrocycles and classify them according ϕ, ψ, and ω torsion angles. In our endeavor to characterize emergent secondary structures, we solved the solid-state structure of the largest metallated cyclic peptoid ever reported, characterized by an unprecedented alternated cis/trans amide bond linkage. Overall, our results indicate that molecules endowed with different elements of asymmetry (central and conformational) provide new architectural elements of facile atroposelective construction and broad conformational stability as the minimalist scaffold for novel stereodefined peptidomimetic foldamers and topologically biased libraries necessary for future application of peptoids in all fields of science.

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.

A versatile strategy for the synthesis of sequence-defined peptoids with side-chain and backbone diversity via amino acid building blocks

Designing artificial macromolecules with absolute sequence order is still a long-term challenge in polymer chemistry as opposed to natural biopolymers with perfectly defined sequences like proteins and DNA. Herein, we combined amino acid building blocks and iterative Ugi reactions for the de novo design and synthesis of sequence-defined peptoids. The highly efficient strategy provided excellent yields and enables multigram-scale synthesis of perfectly defined peptoids. This new strategy furnishes the broad structural diversity of side chains, as well as backbones. Importantly, the overall hydrophobicity and lower critical solution temperature (LCST) behaviours of these precisely defined peptoids can be logically altered by variation of the sequence. By following the same Ugi chemistry, these peptoids are also conjugated to DNA in a simple way, facilitating the development of novel therapeutics.

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.

A study of the cis–trans isomerization preference of N-alkylated peptides containing phosphorus in the side chain and backbone

The current work provides a study on the cis–trans isomerization behaviour of N-alkylated peptides decorated with phosphonate ester groups.

Sequence-defined non-natural polymers: synthesis and applications

Sequence-defined polymer: A promising gateway for the next generation polymeric materials and vast opportunities for new synthetic strategies, functional diversity and its material and biomedical applications.

Genesis of Neuroprotective Peptoid from Aβ30-34 Inhibits Aβ Aggregation and AChE Activity

Aβ peptide and hyper-phosphorylated microtubule associated protein (Tau) aggregation causes severe damage to both the neuron membrane and key signal processing microfilament (microtubule) in Alzheimer's disease (AD) brains. To date, the key challenge is to develop nontoxic, proteolytically stable amyloid inhibitors, which can simultaneously target multiple pathways involved in AD. Various attempts have been made in this direction; however, clinical outcomes of those attempts have been reported to be poor. Thus, we choose development of peptoid (N-substituted glycine oligomers)-based leads as potential AD therapeutics, which are easy to synthesize, found to be proteolytically stable, and exhibit excellent bioavailability. In this paper, we have designed and synthesized a new short peptoid for amyloid inhibition from 30-34 hydrophobic pocket of amyloid beta (Aβ) peptide. The peptoid selectively binds with 17-21 hydrophobic region of Aβ and inhibits Aβ fibril formation. Various in vitro assays suggested that our AI peptoid binds with tubulin/microtubule and promotes its polymerization and stability. This peptoid also inhibits AChE-induced Aβ fibril formation and provides significant neuroprotection against toxicity generated by nerve growth factor (NGF) deprived neurons derived from rat adrenal pheochromocytoma (PC12) cell line. Moreover, this peptoid shows serum stability and is noncytotoxic to primary rat cortical neurons.

A facile on-bead method for fully symmetric tetra-substituted DOTA derivatizations using peptoid moieties

The metal-chelated 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) has made a significant impact on the field of diagnostic imaging. This imaging mechanism is largely dependent on the four side arm functionalities around the DOTA scaffold. We previously demonstrated the effect of peptoid residue modification on these DOTA side arms, thereby conferring diverse physiochemical properties to the imaging mechanism. We generated two on-bead Eu(III)-DOTA libraries with three side arm modifications, where the remaining arm was used to attach DOTA onto the resin. However, having an on-bead fully symmetric tetra-substituted DOTA synthesis route can greatly improve the fields of diagnostic, therapeutic, and theragnostic agent development. Here, we report an efficient method for the synthesis of symmetric tetra-substituted DOTA derivatives by modification with peptoid moieties on all four arms using a conceptually unique solid-phase synthesis approach. Resins with different loading capacities were examined for synthesis feasibility and high loading resins were most effective. The reaction yields were also studied by varying the number of peptoid residues and incorporating different linkers. We have tested the binding ability of the tetra-substituted derivative with its previously tested tri-substituted analogs as model applications. Our protocol provides an efficient and facile on-bead synthesis route for fully symmetric tetra-substituted DOTA derivatizations.

Altering the edge chemistry of bicelles with peptoids

Cell function is tied to the interactions that occur within and across the cell membrane. Therefore, understanding membrane-affiliated interactions is important to many biomedical applications. Advancing the body of knowledge about these interactions will lead to discoveries in biomarker detection and therapeutic targets for disease detection and treatment. Model membrane systems are an effective way to study membrane proteins for such discoveries, allowing for stable protein structure and maintaining native activity. Bicelles, disc-shaped lipid bilayers created by combining long- and short-chain phospholipids, are the model membrane system of focus in this study. Bicelles are accessible from both sides and have a wide size range, which makes them attractive for studying membrane interactions without affecting function. In this work, bicelles were functionalized with peptoids to alter the edge chemistry. Peptoids are suitable for this application because of the large diversity of available side chain chemistries that can be easily incorporated in a sequence-specific manner. The peptoid sequence consists of three functional regions to promote insertion into the edge of bicelles. The insertion sequence at the C-terminus contains two alkyl chains and two hydrophobic, chiral aromatic groups that anchor into the bicelle edge. The facially amphipathic helix contains chiral aromatic groups on one side that interact with the lipid tails and positively charged groups on the other side, which interact with the lipid head groups. Thiol groups are included at the N-terminus to allow for visualization of peptoid location in the bicelle. Bicelle morphology and size were assessed by transmission electron microscopy (TEM) and dynamic light scattering (DLS). Peptoid location in the bicelle was determined by attachment of gold nanoparticles, which confirmed preferential incorporation of the peptoid into the bicelle edge with 82% specificity. Additionally, the peptoid-functionalized bicelles are of similar size and morphology to non-functionalized bicelles. Results from this study show that peptoid-functionalized bicelles are a promising model membrane system with potential applications in biosensors or bioseparations.