Microwave-assisted coupling with DIC/HOBt for the synthesis of difficult peptoids and fluorescently labelled peptides—a gentle heat goes a long way

A study on antimicrobial activity of lysine-like peptoids for the development of new antimicrobials

The development of new medicines with unique methods of antimicrobial action is desperately needed due to the emerging multidrug-resistant bacteria, such as methicillin-resistant Staphylococcus aureus. Therefore, antimicrobial peptoids have emerged as potential new antimicrobials. Thirteen peptoid analogues have been designed and synthesized via solid phase synthesis. These peptoids have undergone a biological analysis to determine the structure-activity relationships that define their antibacterial activity. Each peptoid is composed of nine repeating N-substituted glycine monomers (9-mer). The monomer units were synthesized with three distinct alkyl side chain lengths: four-carbon butyl monomers, six-carbon hexyl monomers, and eight-carbon octyl monomers. Out of 12 different peptoids, only one peptoid called Tosyl-Octyl-Peptoid (TOP) demonstrated significant broad-spectrum bactericidal activity. TOP kills bacteria under non-dividing and dividing conditions. The Minimum Inhibitory Concentrations values of TOP for Staphylococcus epidermidis, Escherichia coli and Klebsiella were 20 µM, whereas Methicillin-resistant Staphylococcus aureus and Methicillin-sensitive Staphylococcus aureus were 40 µM. The highest MIC values were observed for Pseudomonas aeruginosa at 80 µM. The selectivity ratio was calculated, by dividing the 10% haemolysis activity (5 mM) by the median of the MIC (50 µM) yielding a selective ratio for TOP as 100. This selective ratio is well above previously reported peptidomimetics selective ratio of around 20. TOP shows broad-spectrum bactericidal action in both dividing and non-dividing bacteria in co-culture systems and intracellular bacterial killing activity. These results add new information about the antimicrobial peptoids and aid in the future design of synthetic peptoids with increased therapeutic potential.

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.

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.

A combined experimental and computational study on peptide nucleic acid (PNA) analogues of tumor suppressive miRNA-34a

MicroRNAs are a ubiquitous class of non-coding RNAs able to regulate gene expression in diverse biological processes. Widespread miRNAs deregulation was reported in numerous diseases including cancer, with several miRNAs playing oncogenic and/or tumor suppressive role by targeting multiple mRNAs simultaneously. Based on these findings, miRNAs have emerged as promising therapeutic tools for cancer treatment. Herein, for the first time, peptide nucleic acids (PNAs) were studied to develop a new class of molecules able to target 3'UTR on MYCN mRNA without a fully complementary base pairing sequence (as miRNAs). For our proof of concept study we have selected as a model the miRNA-34a, which acts as a tumor suppressor in a number of cancers including neuroblastoma. In particular, miRNA-34a is a direct regulator of MYCN oncogene, whose overexpression is a prominent biomarker for the highly aggressive neuroblastoma phenotype. The design and synthesis of three PNA-based oligomers of different length was described, and their interaction with two binding sites on the target MYCN mRNA was investigated by molecular dynamics simulation, and spectroscopic techniques (CD, UV). Intake assay and confocal microscopy of PNA sequences were also carried out in vitro on neuroblastoma Kelly cells. Despite the presence of multiple mismatches, the PNA/RNA hetero duplexes retain very interesting features in terms of stability, affinity as well as of cellular uptake.

Synthesis and optimization of a reactive oxygen species responsive cellular delivery system

Reactive oxygen species responsive delivery systems for the detection of peroxides in live macrophages have been designed. The oxidative cleavage of a boronic ester to a phenol triggered by hydrogen peroxide followed by self-immolation of a ROS-sensitive cleavable linkervia1,6-elimination allowed the disturbance of the fluorescence resonance energy transfer turning on the near-infrared fluorescence.

Synthesis of acylhydrazino-peptomers, a new class of peptidomimetics, by consecutive Ugi and hydrazino-Ugi reactions

Herein we describe a versatile approach for the synthesis of acylhydrazino-peptomers, a new class of peptidomimetics. The key idea in this approach is based on a simple route using a one-pot hydrazino-Ugi four-component reaction followed by a hydrazinolysis or hydrolysis reaction and subsequent hydrazino-Ugi reaction or classical Ugi reaction for the construction of acyclic acylhydrazino-peptomers. The consecutive multicomponent reactions produced a variety of acylhydrazino-peptomers in moderate to excellent yields (47–90%). These compounds are multifunctional intermediates that can be further functionalized to obtain new peptidomimetics with potential biological activity.

Fluorogenic Substrates for In Situ Monitoring of Caspase-3 Activity in Live Cells

The in situ detection of caspase-3 activity has applications in the imaging and monitoring of multiple pathologies, notably cancer. A series of cell penetrating FRET-based fluorogenic substrates were designed and synthesised for the detection of caspase-3 in live cells. A variety of modifications of the classical caspase-3 and caspase-7 substrate sequence Asp-Glu-Val-Asp were carried out in order to increase caspase-3 affinity and eliminate caspase-7 cross-reactivity. To allow cellular uptake and good solubility, the substrates were conjugated to a cationic peptoid. The most selective fluorogenic substrate 27, FAM-Ahx-Asp-Leu-Pro-Asp-Lys(MR)-Ahx, conjugated to the cell penetrating peptoid at the C-terminus, was able to detect and quantify caspase-3 activity in apoptotic cells without cross-reactivity by caspase-7.

Convergent chemo-enzymatic synthesis of mannosylated glycopeptides; targeting of putative vaccine candidates to antigen presenting cells

The combination of solid phase peptide synthesis and endo-β-N-acetylglucosaminidase (ENGase) catalysed glycosylation is a powerful convergent synthetic method allowing access to glycopeptides bearing full-length N-glycan structures. Mannose-terminated N-glycan oligosaccharides, produced by either total or semi-synthesis, were converted into oxazoline donor substrates. A peptide from the human cytomegalovirus (CMV) tegument protein pp65 that incorporates a well-characterised T cell epitope, containing N-acetylglucosamine at specific Asn residues, was accessed by solid phase peptide synthesis, and used as an acceptor substrate. High-yielding enzymatic glycosylation afforded glycopeptides bearing defined homogeneous high-mannose N-glycan structures. These high-mannose containing glycopeptides were tested for enhanced targeting to human antigen presenting cells (APCs), putatively mediated via the mannose receptor, and for processing by the APCs for presentation to human CD8+ T cells specific for a 9-mer epitope within the peptide. Binding assays showed increased binding of glycopeptides to APCs compared to the non-glycosylated control. Glycopeptides bearing high-mannose N-glycan structures at a single site outside the T cell epitope were processed and presented by the APCs to allow activation of a T cell clone. However, the addition of a second glycan within the T cell epitope resulted in ablation of T cell activation. We conclude that chemo-enzymatic synthesis of mannosylated glycopeptides enhances uptake by human APCs while preserving the immunogenicity of peptide epitopes within the glycopeptides, provided those epitopes are not themselves glycosylated.

Cell-penetrating peptoids: introduction of novel cationic side chains

During the last decade peptoid-based molecular transporters have been broadly applied. They are highly valued for their easy synthesis and their superior stability against enzymatic degradation. The special structure of peptoids generally allows introducing a variety of different side chains. Yet, the cationic side chains of cell-penetrating peptoids displayed solely lysine- or arginine-like structures. Thus this report is intended to extend the spectrum of cationic peptoid side chains. Herein, we present novel functional groups, like polyamines, aza-crown ethers, or triphenylphosphonium ions that are introduced into peptoids for the first time. In addition, the obtained peptoids were tested for their cell-penetrating properties.

Rhodamine F: a novel class of fluorous ponytailed dyes for bioconjugation

Incorporation of fluorous ponytails such as polyfluorinated alkyl residues (CH2)m(CF2)nCF3 leads to a novel class of bright rhodamine-based fluorescence dyes. These dyes combine the excellent photophysical properties of the frequently used rhodamine dyes with the unique features of "light" fluorous molecules. One of those features is the possibility to separate substances utilizing fluorous solid-phase extraction (F-SPE), which is based on the specific intermolecular interaction between fluorous compounds. Thus, molecules, which are labeled with these new dyes, are not only accessible to fluorescence experiments, but can also be easily purified (via so-called FluoroFlash columns) prior to use. The dyes were bound to a cell penetrating peptoid (polycationic oligo(N-substituted) glycine) on solid supports. These conjugates were purified with F-SPE before their photophysical and biological properties were investigated.

The synthesis and application of Fmoc-Lys(5-Fam) building blocks

Fluorescence resonance energy transfer (FRET) peptide substrates are often utilized for protease activity assays. This study has examined the preparation of FRET triple-helical peptide (THP) substrates using 5-carboxyfluorescein (5-Fam) as the fluorophore and 4,4-dimethylamino-azobenzene-4'-carboxylic acid (Dabcyl) as the quencher. The N(α)-(9-fluorenylmethoxycarbonyl)-N(ε)-(5-carboxyfluorescein)-L-lysine [Fmoc-Lys(5-Fam)] building block was synthesized utilizing two distinct synthetic routes. The first involved copper complexation of Lys while the second utilized Fmoc-Lys with microwave irradiation. Both approaches allowed convenient production of a very pure final product at a reasonable cost. Fmoc-Lys(5-Fam) and Fmoc-Lys(Dabcyl) were incorporated into the sequence of a THP substrate utilizing automated solid-phase peptide synthesis protocols. A second substrate was assembled where (7-methoxycoumarin-4-yl)-acetyl (Mca) was the fluorophore and 2,4-dinitrophenyl (Dnp) was the quencher. Circular dichroism spectroscopy was used to determine the influence of the fluorophore/quencher pair on the stability of the triple-helix. The activity of the two substrates was examined with three matrix metalloproteinases (MMPs), MMP-1, MMP-13, and MT1-MMP. The combination of 5-Fam as fluorophore and Dabcyl as quencher resulted in a triple-helical substrate that, compared with the fluorophore/quencher pair of Mca/Dnp, had a slightly destabilized triple-helix but was hydrolyzed more rapidly by MMP-1 and MMP-13 and had greater sensitivity.

Peptoid polymers: a highly designable bioinspired material

Bioinspired polymeric materials are attracting increasing attention due to significant advantages over their natural counterparts: the ability to precisely tune their structures over a broad range of chemical and physical properties, increased stability, and improved processability. Polypeptoids, a promising class of bioinspired polymer based on a N-substituted glycine backbone, have a number of unique properties that bridge the material gap between proteins and bulk polymers. Peptoids combine the sequence specificity of biopolymers with the simpler intra/intermolecular interactions and robustness of traditional synthetic polymers. They are highly designable because hundreds of chemically diverse side chains can be introduced from simple building blocks. Peptoid polymers can be prepared by two distinct synthetic techniques offering access to two material subclasses: (1) automated solid-phase synthesis which enables precision sequence control and near absolute monodispersity up to chain lengths of ~50 monomers, and (2) a classical polymerization approach which allows access to higher molecular weights and larger-scale yields, but with less control over length and sequence. This combination of facile synthetic approaches makes polypeptoids a highly tunable, rapid polymer prototyping platform to investigate new materials that are intermediate between proteins and bulk polymers, in both their structure and their properties. In this paper, we review the methods to synthesize peptoid polymers and their applications in biomedicine and nanoscience, as both sequence-specific materials and as bulk polymers.

Cell Penetrating Peptoids (CPPos): Synthesis of a Small Combinatorial Library by Using IRORI MiniKans

Cell penetrating peptoids (CPPos) are potent mimics of the corresponding cell penetrating peptides (CPPs). The synthesis of diverse oligomeric libraries that display a variety of backbone scaffolds and side-chain appendages are a very promising source of novel CPPos, which can be used to either target different cellular organelles or even different tissues and organs. In this study we established the submonomer-based solid phase synthesis of a “proof of principle” peptoid library in IRORI MiniKans to expand the amount for phenotypic high throughput screens of CPPos. The library consisting of tetrameric peptoids [oligo(N-alkylglycines)] was established on Rink amide resin in a split and mix approach with hydrophilic and hydrophobic peptoid side chains. All CPPos of the presented library were labeled with rhodamine B to allow for the monitoring of cellular uptake by fluorescent confocal microscopy. Eventually, all the purified peptoids were subjected to live cell imaging to screen for CPPos with organelle specificity. While highly charged CPPos enter the cells by endocytosis with subsequent endosomal release, critical levels of lipophilicity allow other CPPos to specifically localize to mitochondria once a certain lipophilicity threshold is reached.

The use of solid supports to generate nucleic acid carriers

Nucleic acids are the foundation stone of all cellular processes. Consequently, the use of DNA or RNA to treat genetic and acquired disorders (so called gene therapy) offers enormous potential benefits. The restitution of defective genes or the suppression of malignant genes could target a range of diseases, including cancers, inherited diseases (cystic fibrosis, muscular dystrophy, etc.), and viral infections. However, this strategy has a major barrier: the size and charge of nucleic acids largely restricts their transit into eukaryotic cells. Potential strategies to solve this problem include the use of a variety of natural and synthetic nucleic acid carriers. Driven by the aim and ambition of translating this promising therapeutic approach into the clinic, researchers have been actively developing advanced delivery systems for nucleic acids for more than 20 years. A decade ago we began our investigations of solid-phase techniques to construct families of novel nucleic acid carriers for transfection. We envisaged that the solid-phase synthesis of polycationic dendrimers and derivatized polyamimes would offer distinct advantages over solution phase techniques. Notably in solid phase synthesis we could take advantage of mass action and streamlined purification procedures, while simplifying the handling of compounds with high polarities and plurality of functional groups. Parallel synthesis methods would also allow rapid access to libraries of compounds with improved purities and yields over comparable solution methodologies and facilitate the development of structure activity relationships. We also twisted the concept of the solid-phase support on its head: we devised miniaturized solid supports that provided an innovative cell delivery vehicle in their own right, carrying covalently conjugated cargos (biomolecules) into cells. In this Account, we summarize the main outcomes of this series of chemically related projects.

Novel pyridinium dyes that enable investigations of peptoids at the single-molecule level

Single-molecule microscopy is a powerful tool for investigating various uptake mechanisms of cell-penetrating biomolecules. A particularly interesting class of potential transporter molecules are peptoids. Fluorescence labels for such experiments need to comply with several physical, chemical, and biological requirements. Herein, we report the synthesis and photophysical investigation of new fluorescent pyridinium derived dyes. These fluorescent labels have advantageous structural variations and spacer units in order to avoid undesirable interactions with the labeled molecule and are able to easily functionalize biomolecules. In our case, cell-penetrating peptoids are successfully labeled on solid supports, and in ensemble measurements the photophysical properties of the dyes and the fluorescently labeled peptoids are investigated. Both fluorophores and peptoids are imaged at the single-molecule level in thin polymer gels. With respect to bleaching times and fluorescence lifetimes the dye molecules and the peptoids show only slightly perturbed optical behaviors. These investigations indicate that the new fluorophores fulfill well single-molecule microscopy and solid-phase synthesis requirements.

Solid-phase synthesis of N-substituted glycine oligomers (alpha-peptoids) and derivatives

Peptoids (N-substituted polyglycines and extended peptoids with variant backbone amino-acid monomer units) are oligomeric synthetic polymers that are becoming a valuable molecular tool in the biosciences. Of particular interest are their applications to the exploration of peptoid secondary structures and drug design. Major advantages of peptoids as research and pharmaceutical tools include the ease and economy of synthesis, highly variable backbone and side-chain chemistry possibilities. At the same time, peptoids have been demonstrated as highly active in biological systems while resistant to proteolytic decay. This review with 227 references considers the solid-phase synthetic aspects of peptoid preparation and utilization up to 2010 from the instigation, by R. N. Zuckermann et al., of peptoid chemistry in 1992.

Efficient inhibition of miR-155 function in vivo by peptide nucleic acids

MicroRNAs (miRNAs) play an important role in diverse physiological processes and are potential therapeutic agents. Synthetic oligonucleotides (ONs) of different chemistries have proven successful for blocking miRNA expression. However, their specificity and efficiency have not been fully evaluated. Here, we show that peptide nucleic acids (PNAs) efficiently block a key inducible miRNA expressed in the haematopoietic system, miR-155, in cultured B cells as well as in mice. Remarkably, miR-155 inhibition by PNA in primary B cells was achieved in the absence of any transfection agent. In mice, the high efficiency of the treatment was demonstrated by a strong overlap in global gene expression between B cells isolated from anti-miR-155 PNA-treated and miR-155-deficient mice. Interestingly, PNA also induced additional changes in gene expression. Our analysis provides a useful platform to aid the design of efficient and specific anti-miRNA ONs for in vivo use.

Semi-automated microwave-assisted SPPS: Optimization of protocols and synthesis of difficult sequences

Precise microwave heating has emerged as a valuable addition to solid-phase peptide synthesis. New methods and protocols are required to utilize this potential and make it a reliable technique. Here, we describe a new semi-automated instrument for solid-phase peptide synthesis with microwave heating and report protocols for its reliable use. The instrument features a flow-through reaction vessel that is placed in the microwave instrument throughout the synthesis. Bubbling with N(2) gas during the microwave irradiation proved important for temperature control. Washing and Fmoc removal steps were automated, while activated Fmoc-amino acids were added manually. Several linkers and resins were evaluated and protocols for synthesis of difficult sequences were developed. These included on-resin reductive amination of BAL handles under microwave heating. We believe that the instrument, as well as the protocols for its use, will be useful tools for peptide chemists.

Strategies for the preparation of synthetic transfection vectors

In the late 1980s independent work by Felgner and Behr pioneered the use of cationic materials to complex and deliver nucleic acids into eukaryotic cells. Since this time, a vast number of synthetic transfection vectors, which are typically divided into two main "transfectors", have been developed namely: (1) cationic lipids and (2) polycationic polymers. In this chapter the main synthetic approaches used for the synthesis of these compounds will be reviewed with particular attention paid to: cationic lipids and dendrimers. This review is aimed primarily at the younger audience of doctoral students and non-specialist readers.

Passage of Trojan peptoids into plant cells

Efficient drug delivery is essential for many therapeutic applications. In this context, Trojan peptoids have attracted attention as powerful tools to deliver bioactive molecules into living cells. Certain cell-penetrating peptides, peptide mimetics, and peptoids have been shown to be endowed with a transport function and the structural features of this function have been characterized. However, most of the research has been done by using mammalian cell cultures as model organisms and the actual cellular mechanism of membrane passage has not been elucidated. Plant cells, which are encased in a cellulosic cell wall and differ in membrane composition, represent an alternative experimental system to address this issue, but so far, have attracted only little attention for both peptide- and peptoid-based carrier systems. Moreover, efficient delivery of nonproteinaceous bioactive macromolecules into living plant cells could complement genetic engineering in biotechnological applications, such as metabolic engineering and molecular farming. In the present study, we investigated carrier peptoids with or without guanidinium side chains with regard to their uptake into plant cells, the cellular mechanism of uptake, and intracellular localization. We can show that in contrast to polyamine peptoids (polylysine-like) fluorescently labeled polyguanidine peptoids (polyarginine-like) enter rapidly into tobacco BY-2 cells without affecting the viability of these cells. A quantitative comparison of this uptake with endocytosis of fluorescently labeled dextranes indicates that the main uptake of the guanidinium peptoids occurs between 30-60 min after the start of incubation and clearly precedes endocytosis. Dual visualization with the endosomal marker FM4-64 shows that the intracellular guanidinium peptoid is distinct from endocytotic vesicles. Once the polyguanidine peptoids have entered the cell, they associate with actin filaments and microtubules. By pharmacological manipulation of the cytoskeleton we tested whether the association with the cytoskeleton is necessary for uptake, and observed that the actin inhibitor latrunculin B as well as the microtubule inhibitor oryzalin impaired uptake and intracellular spread of the guanidinium carrier to a certain extent. These findings are discussed with respect to the potential mechanisms of uptake and with respect to the potential of Trojan peptoids as tools for metabolic engineering in plant biotechnology.

Altered activity and physicochemical properties of short cationic antimicrobial peptides by incorporation of arginine analogues

The incorporation of nongenetically encoded amino acids is a well established strategy to alter the behavior of several types of promising cationic antimicrobial peptides. Generally, these elements have been improved mimics of the hydrophobic amino acids yielding peptides with increased stability and potency. In this initial study, the effect of systematic replacement of Arg in a well-defined moderately antimicrobial tripeptide library is described. It is shown that the arginine analogues need to display a strong basicity to produce active peptides. It is further revealed that the hydrophobic units needed for activity in these peptides can be effectively incorporated in the direct vicinity of the cationic charge to produce compounds with improved antibacterial properties. A well-defined facial amphiphilic structure, which remains intact upon introduction of hydrophobic elements in the cationic side chains, is seen for the majority of the tested peptides. Microcalorimetric studies revealed a peptide binding to large anionic unilamellar vesicles (LUVs) mimicking the Gram-positive bacterial membrane as well as a potentially competitive binding to human serum albumin in the low- to mid-micromolar range. No considerable alterations in binding to either albumin or the LUVs were seen for the analogue containing peptides. A neutral LUV mimicking the eukaryotic cell membrane showed no significant binding to any of the peptides. The oral absorption of this class of short lactoferricin based peptides was investigated for the first time and revealed that incorporation of weaker bases than Arg produced peptides with much improved permeability in a recently developed permeation model, the phospholipid vesicle based barrier assay. Collectively, the results presented here show that there is ample room to toggle the activity and physical properties of short cationic antimicrobial peptides by incorporation of arginine analogues.

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

Oligomers of N-substituted glycine, or peptoids, are versatile tools to probe biological processes and hold promise as therapeutic agents. An underlying theme in the majority of recent peptoid research is the connection between peptoid function and peptoid structure. For certain applications, well-folded peptoids are essential for activity, while unstructured peptoids appear to suffice, or even are superior, for other applications. Currently, these structure-function connections are largely made after the design, synthesis, and characterization process. However, as guidelines for peptoid folding are elucidated and the known biological activities are expanded, we anticipate these connections will provide a pathway toward the de novo design of functional peptoids. In this perspective, we review several of the peptoid structure-function relationships that have been delineated over the past five years.

Synthesis, penetrability and intracellular targeting of fluorescein-tagged peptoids and peptide-peptoid hybrids

The search for novel, generally applicable and highly efficient delivery tools is a major activity in the biotechnology arena. Using highly optimized microwave based solid-phase chemistry a series of fluorescein-labelled cationic peptoid conjugates were synthesized within 24h and cellular uptake into HeLa, L929 and K562 cells examined via flow cytometry. As expected, analysis revealed that longer oligomers achieved greater cellular penetration (7e (9 mer)>7d (7 mer)>7c (5 mer)>7b (3 mer)>7a (1 mer)) with the nonamer 7e proving to be a remarkable vehicle for all the cell lines, showing excellent penetrability into K562 and L929 cells and extraordinary cell delivery into HeLa cells. Confocal microscopy showed that the hybrid peptoid-nuclear localizing sequence (PKKKRKV from the simian virus 40 large T antigen) resulted in very high levels of nuclei delivery after 3h, opening up a range of applications such as nuclei staining of living cells with non-DNA-intercalating fluorescent probes.

From 10,000 to 1: Selective synthesis and enzymatic evaluation of fluorescence resonance energy transfer peptides as specific substrates for chymopapain

The synthesis and detailed enzymatic analysis of fluorescence resonance energy transfer (FRET)-based peptides as substrates for chymopapain are reported. The design of these substrates arose from a massively parallel high-throughput microarray screening process using peptide nucleic acid (PNA) encoding technology, allowing the identification of detailed substrate specificities of any protease. Two peptides so identified with chymopapain were observed to be excellent substrates with low micromolar K(m) values and turnover numbers on the order of hundreds per second. Mass spectroscopy studies showed unequivocally the specificity of chymopapain toward Ala, Pro, Val, and Lys for positions P(4) to P(1) while not presenting high specificity for residues in position P(1)'.

Effect of microwave radiation on enzymatic and chemical Peptide bond synthesis on solid phase

Peptide bond synthesis was performed on PEGA beads under microwave radiations. Classical chemical coupling as well as thermolysin catalyzed synthesis was studied, and the effect of microwave radiations on reaction kinetics, beads' integrity, and enzyme activity was assessed. Results demonstrate that microwave radiations can be profitably exploited to improve reaction kinetics in solid phase peptide synthesis when both chemical and biocatalytic strategies are used.

Very long-chain fatty tails for enhanced transfection

The long chain saturated fatty acids, arachidic (C20) and lignoceric (C24), are found as components of phospholipids within mammalian cellular membranes. Although these lipids have rarely been used as components of transfection reagents, we recently demonstrated that elongation of the fatty tail beyond C18 provide a means of increasing the transfection efficiency of cationic lipids. To investigate this effect further, a new library of single-chained cationic lipids consisting of mono-, di- or tri-arginine residues, a range of amino acid spacers and these long-chain saturated fatty tails were synthesised using an Fmoc solid-phase strategy, which allowed the preparation of 18 compounds, some with remarkable transfection abilities.

Rapid solid-phase synthesis of a calmodulin-binding peptide using controlled microwave irradiation

A rapid and efficient microwave-assisted solid-phase synthesis method for the preparation of a nonapeptide using conventional Fmoc/Bu(t) orthogonal protection strategy is described. In this protocol, the coupling steps are performed within 5 min at 60 degrees C and the Fmoc-deprotection steps are completed within 3 min at 60 degrees C using a dedicated single-mode microwave peptide synthesizer utilizing temperature-controlled conditions. It is demonstrated that the model nonapeptide (containing the calmodulin-binding octapeptide sequence) is synthesized in a shorter time (approximately 3.5 h) and with high purity (>95%) under microwave irradiation conditions in comparison with a reference peptide that is obtained by standard methods at room temperature (within 11 h).