Towards functional bionanomaterials based on self-assembling cyclic peptide nanotubes

Self-Assembled Peptide with Morphological Structure for Bioapplication

Peptide materials, such as self-assembled peptide materials, are very important biomaterials. Driven by multiple interaction forces, peptide molecules can self-assemble into a variety of different macroscopic forms with different properties and functions. In recent years, the research on self-assembled peptides has made great progress from laboratory design to clinical application. This review focuses on the different morphologies, including nanoparticles, nanovesicles, nanotubes, nanofibers, and others, formed by self-assembled peptide. The mechanisms and applications of the morphology transformation are also discussed in this paper, and the future direction of self-assembled nanomaterials is envisioned.

Comprehensive Study of Artificial Light-Harvesting Systems with a Multi-Step Sequential Energy Transfer Mechanism

Artificial light-harvesting systems (LHSs) with a multi-step sequential energy transfer mechanism significantly enhance light energy utilization. Nonetheless, most of these systems exhibit an overall energy transfer efficiency below 80%. Moreover, due to challenges in molecularly aligning multiple donor/acceptor chromophores, systems featuring ≥3-step sequential energy transfer are rarely reported. Here, a series of artificial LHSs is introduced featuring up to 4-step energy transfer mechanism, constructed using a cyclic peptide-based supramolecular scaffold. These LHSs showed remarkably high energy transfer efficiencies (≥90%) and satisfactory fluorescence quantum yields (ranging from 17.6% to 58.4%). Furthermore, the structural robustness of the supramolecular scaffold enables a comprehensive study of these systems, elucidating the associated energy transfer pathways, and identifying additional energy transfer processes beyond the targeted sequential energy transfer. Overall, this comprehensive investigation not only enhances the understanding of these LHSs, but also underscores the versatility of cyclic peptide-based supramolecular scaffolds in advancing energy harvesting technologies.

Supra-Fluorophores: Ultrabright Fluorescent Supramolecular Assemblies Derived from Conventional Fluorophores in Water

Fluorescent organic nanoparticles (NPs) with exceptional brightness hold significant promise for demanding fluorescence bioimaging applications. Although considerable efforts are invested in developing novel organic dyes with enhanced performance, augmenting the brightness of conventional fluorophores is still one of the biggest challenges to overcome. This study presents a supramolecular strategy for constructing ultrabright fluorescent nanoparticles in aqueous media (referred to as "Supra-fluorophores") derived from conventional fluorophores. To achieve this, this course has employed a cylindrical nanoparticle with a hydrophobic microdomain, assembled by a cyclic peptide-diblock copolymer conjugate in water, as a supramolecular scaffold. The noncovalent dispersion of fluorophore moieties within the hydrophobic microdomain of the scaffold effectively mitigates the undesired aggregation-caused quenching and fluorescence quenching by water, resulting in fluorescent NPs with high brightness. This strategy is applicable to a broad spectrum of fluorophore families, covering polyaromatic hydrocarbons, coumarins, boron-dipyrromethenes, cyanines, xanthenes, and squaraines. The resulting fluorescent NPs demonstrate high fluorescence quantum yield (>30%) and brightness per volume (as high as 12 060 m-1 cm-1 nm-3). Moreover, high-performance NPs with emission in the NIR region are constructed, showcasing up to 20-fold increase in both brightness and photostability. This Supra-fluorophore strategy offers a versatile and effective method for transforming existing fluorophores into ultrabright fluorescent NPs in aqueous environments, for applications such as bioimaging.

The influence of backbone fluorination on the helicity of α/γ-hybrid peptides

Peptides that are composed of an alternating pattern of α- and γ-amino acids are potentially valuable as metabolism-resistant bioactive agents. For optimal function, some kind of conformational restriction is usually required to either stabilize the dominant 12-helix, or else to divert the peptide away from this conformation in a controlled way. Herein, we explore stereoselective fluorination as a method for controlling the conformations of α/γ-hybrid peptides. We show through a combination of X-ray, NMR and CD analyses that fluorination can either stabilize or disrupt the 12-helix, depending on the fluorine stereochemistry. These findings could inform the ongoing development of diverse functional hybrid peptides.

Supra-Cyanines: Ultrabright Cyanine-Based Fluorescent Supramolecular Materials in Solution and in the Solid State

Fluorescent materials with high brightness play a crucial role in the advancement of various technologies such as bioimaging, photonics, and OLEDs. While significant efforts are dedicated to designing new organic dyes with improved performance, enhancing the brightness of existing dyes holds equal importance. In this study, we present a simple supramolecular strategy to develop ultrabright cyanine-based fluorescent materials by addressing long-standing challenges associated with cyanine dyes, including undesired cis-trans photoisomerization and aggregation-caused quenching. Supra-cyanines are obtained by incorporating cyanine moieties in a cyclic peptide-based supramolecular scaffold, and exhibit high fluorescence quantum yields (up to 50 %) in both solution and in the solid state. These findings offer a versatile approach for constructing highly emissive cyanine-based supramolecular materials.

Intracellular Zn(II) induced turn-on fluorescence of an L-phenylalanine-derived pseudopeptide

A C2 symmetric L-phenylalanine-derived pseudopeptide has been synthesized for selective and sensitive recognition of Zn(II) ions in aqueous-organic media. The pseudopeptidic probes exhibit intracellular Zn(II) ion-sensing capabilities as demonstrated via live-cell fluorescence studies on RAW264.7 cells. Hence, we present a bioinspired pseudopeptide for potential biological applications involving intracellular Zn(II) ion detection.

Supramolecular peptide nanotubes as artificial enzymes for catalysing ester hydrolysis

Peptide-based artificial enzymes are attracting significant interest because of their remarkable resemblance in both composition and structure to native enzymes. Herein, we report the construction of histidine-containing cyclic peptide-based supramolecular polymeric nanotubes to function as artificial enzymes for ester hydrolysis. The optimized catalyst shows a ca. 70-fold increase in reaction rate compared to the un-catalysed reaction when using 4-nitrophenyl acetate as a model substrate. Furthermore, the amphiphilic nature of the supramolecular catalysts enables an enhanced catalytic activity towards hydrophobic substrates. By incorporating an internal hydrophobic region within the self-assembled polymeric nanotube, we achieve a 55.4-fold acceleration in hydrolysis rate towards a more hydrophobic substrate, 4-nitrophenyl butyrate. This study introduces supramolecular peptide nanotubes as an innovative class of supramolecular scaffolds for fabricating artificial enzymes with better structural and chemical stability, catalysing not only ester hydrolysis, but also a broader spectrum of catalytic reactions.

β-Turn Induction by a Diastereopure Azepane-Derived Quaternary Amino Acid

β-Turns are one of the most common secondary structures found in proteins. In the interest of developing novel β-turn inducers, a diastereopure azepane-derived quaternary amino acid has been incorporated into a library of simplified tetrapeptide models in order to assess the effect of the azepane position and peptide sequence on the stabilization of β-turns. The conformational analysis of these peptides by molecular modeling, NMR spectroscopy, and X-ray crystallography showed that this azepane amino acid is an effective β-turn inducer when incorporated at the i + 1 position. Moreover, the analysis of the supramolecular self-assembly of one of the β-turn-containing peptide models in the solid state reveals that it forms a supramolecular helical arrangement while maintaining the β-turn structure. The results here presented provide the basis for the use of this azepane quaternary amino acid as a strong β-turn inducer in the search for novel peptide-based bioactive molecules, catalysts, and biomaterials.

Dynamic Control of Cyclic Peptide Assembly to Form Higher-Order Assemblies

Chirality correction, asymmetry, ring-chain tautomerism and hierarchical assemblies are fundamental phenomena in nature. They are geometrically related and may impact the biological roles of a protein or other supermolecules. It is challenging to study those behaviors within an artificial system due to the complexity of displaying these features. Herein, we design an alternating D,L peptide to recreate and validate the naturally occurring chirality inversion prior to cyclization in water. The resulting asymmetrical cyclic peptide containing a 4-imidazolidinone ring provides an excellent platform to study the ring-chain tautomerism, thermostability and dynamic assembly of the nanostructures. Different from traditional cyclic D,L peptides, the formation of 4-imidazolidinone promotes the formation of intertwined nanostructures. Analysis of the nanostructures confirmed the left-handedness, representing chirality induced self-assembly. This proves that a rationally designed peptide can mimic multiple natural phenomena and could promote the development of functional biomaterials, catalysts, antibiotics, and supermolecules.

Simple Complexity: Incorporating Bioinspired Delivery Machinery within Self-Assembled Peptide Biogels

Bioinspired self-assembly is a bottom-up strategy enabling biologically sophisticated nanostructured biogels that can mimic natural tissue. Self-assembling peptides (SAPs), carefully designed, form signal-rich supramolecular nanostructures that intertwine to form a hydrogel material that can be used for a range of cell and tissue engineering scaffolds. Using the tools of nature, they are a versatile framework for the supply and presentation of important biological factors. Recent developments have shown promise for many applications such as therapeutic gene, drug and cell delivery and yet are stable enough for large-scale tissue engineering. This is due to their excellent programmability—features can be incorporated for innate biocompatibility, biodegradability, synthetic feasibility, biological functionality and responsiveness to external stimuli. SAPs can be used independently or combined with other (macro)molecules to recapitulate surprisingly complex biological functions in a simple framework. It is easy to accomplish localized delivery, since they can be injected and can deliver targeted and sustained effects. In this review, we discuss the categories of SAPs, applications for gene and drug delivery, and their inherent design challenges. We highlight selected applications from the literature and make suggestions to advance the field with SAPs as a simple, yet smart delivery platform for emerging BioMedTech applications.

Triple Thorpe-Ingold Effect in the Synthesis of 18-Membered C3 Symmetric Lactams Stacking as Endless Supramolecular Tubes

Three C₃ symmetric macrolactams were very efficiently cyclized from their linear precursors. Adequately located substituents are responsible for the enhancement of reactivity that is not observed in the unsubstituted parent. DFT calculations show that the properly folded cyclization precursor, the reactive conformer, is more populated than other conformers, leading to a decrease of free energy of activation. The crystal structure of the ring substituted with three very bulky esters indicates that tubular stacking is preserved.

Multifunctional Self-Assembled Peptide Hydrogels for Biomedical Applications

Self-assembly is a growth mechanism in nature to apply local interactions forming a minimum energy structure. Currently, self-assembled materials are considered for biomedical applications due to their pleasant features, including scalability, versatility, simplicity, and inexpensiveness. Self-assembled peptides can be applied to design and fabricate different structures, such as micelles, hydrogels, and vesicles, by diverse physical interactions between specific building blocks. Among them, bioactivity, biocompatibility, and biodegradability of peptide hydrogels have introduced them as versatile platforms in biomedical applications, such as drug delivery, tissue engineering, biosensing, and treating different diseases. Moreover, peptides are capable of mimicking the microenvironment of natural tissues and responding to internal and external stimuli for triggered drug release. In the current review, the unique characteristics of peptide hydrogels and recent advances in their design, fabrication, as well as chemical, physical, and biological properties are presented. Additionally, recent developments of these biomaterials are discussed with a particular focus on their biomedical applications in targeted drug delivery and gene delivery, stem cell therapy, cancer therapy and immune regulation, bioimaging, and regenerative medicine.

Self-healing cyclic peptide hydrogels

Hydrogels are soft materials of great interest in different areas such as chemistry, biology, and therapy. Gels made by the self-assembly of small molecules are known as supramolecular gels. The modulation of their properties by monomer molecular design is still difficult to predict due to the potential impact of subtle structural modifications in the self-assembly process. Herein, we introduce the design principles of a new family of self-assembling cyclic octapeptides of alternating chirality that can be used as scaffolds for the development of self-healing hydrogelator libraries with tunable properties. The strategy was used in the preparation of an amphiphilic cyclic peptide monomer bearing an alkoxyamine connector, which allowed the insertion of different aromatic aldehyde pendants to modulate the hydrophobic/hydrophilic balance and fine-tune the properties of the resulting gel. The resulting amphiphiles were able to form self-healable hydrogels with viscoelastic properties (loss tangent, storage modulus), which were strongly dependent on the nature and number of aromatic moieties anchored to the hydrophilic peptide. Structural studies by SEM, STEM and AFM indicated that the structure of the hydrogels was based on a dense network of peptide nanotubes. Excellent agreement was established between the peptide primary structure, nanotube length distributions and viscoelastic behaviour.

Rip it, stitch it, click it: A Chemist's guide to VLP manipulation

Viruses are some of nature's most ubiquitous self-assembled molecular containers. Evolutionary pressures have created some incredibly robust, thermally, and enzymatically resistant carriers to transport delicate genetic information safely. Virus-like particles (VLPs) are human-engineered non-infectious systems that inherit the parent virus' ability to self-assemble under controlled conditions while being non-infectious. VLPs and plant-based viral nanoparticles are becoming increasingly popular in medicine as their self-assembly properties are exploitable for applications ranging from diagnostic tools to targeted drug delivery. Understanding the basic structure and principles underlying the assembly of higher-order structures has allowed researchers to disassemble (rip it), reassemble (stitch it), and functionalize (click it) these systems on demand. This review focuses on the current toolbox of strategies developed to manipulate these systems by ripping, stitching, and clicking to create new technologies in the biomedical space.

Synthesis of Cyclotetrapeptides Analogues to Natural Products as Herbicides

The synthesis of cyclotetrapeptides analogues of the natural products tentoxin and versicotide D was achieved in good yield by solid phase peptide synthesis (SPPS) of their linear precursors and solution phase cyclization. All the cyclopeptides and several open precursors were evaluated as herbicides. Five cyclopeptides and five lineal peptides showed a significant inhibition (>70%) of Ryegrass seed’s radicle growth at 67 μg/mL. The evaluation at lower concentrations (4−11 μM) indicates two cyclopeptides analogs of tentoxin, which present one (N-Methyl-d-Phe), and two N-MeAA (N-Methyl-Ala and N-Methyl-Phe), respectively, as the most active of them, showing remarkable phytotoxic activity. In two cases, the open precursors are as active as their corresponding cyclopeptide. However, many linear peptides are inactive and their cyclization derivatives showed herbicidal activity. In addition, two cyclopeptide analogues of versicotide D showed more improved activity than the natural product. The results indicate that the peptide sequence, the amino acid stereochemistry and the presence of N-methyl group have important influence on the phytotoxic activity. Moreover, several compounds could be considered as lead candidates in the development of bioherbicides.

Synthetic Receptors Based on Abiotic Cyclo(pseudo)peptides

Work on the use of cyclic peptides or pseudopeptides as synthetic receptors started even before the field of supramolecular chemistry was firmly established. Research initially focused on the development of synthetic ionophores and involved the use of macrocycles with a repeating sequence of subunits along the ring to facilitate the correlation between structure, conformation, and binding properties. Later, nonnatural amino acids as building blocks were also considered. With growing research in this area, cyclopeptides and related macrocycles developed into an important and structurally diverse receptor family. This review provides an overview of these developments, starting from the early years. The presented systems are classified according to characteristic structural elements present along the ring. Wherever possible, structural aspects are correlated with binding properties to illustrate how natural or nonnatural amino acids affect binding properties.

Tailoring the luminescence of FRET systems built using supramolecular polymeric nanotubes

Supramolecular polymeric nanotubes self-assembled from cyclic peptide–polymer conjugates are employed as general scaffolds to fabricate supramolecular FRET systems with tailorable and responsive luminescence.

1D alignment of proteins and other nanoparticles by using reversible covalent bonds on cyclic peptide nanotubes

Peptide nanotubes deposit on mica surface can be used for the alignment of proteins thank to the use of dynamic covalent bonds that allow the incorporation of appropriate ligands on nanotube surface.

Mechanism of Side Chain-Controlled Proton Conductivity in Bioinspired Peptidic Nanostructures

Bioinspired peptide assemblies are promising candidates for use as proton-conducting materials in electrochemical devices and other advanced technologies. Progress toward applications requires establishing foundational structure-function relationships for transport in these materials. This experimental-theoretical study sheds light on how the molecular structure and proton conduction are linked in three synthetic cyclic peptide nanotube assemblies that comprise the three canonical basic amino acids (lysine, arginine, and histidine). Experiments find an order of magnitude higher proton conductivity for lysine-containing peptide assemblies compared to histidine and arginine containing assemblies. The simulations indicate that, upon peptide assembly, the basic amino acid side chains are close enough to enable direct proton transfer. The proton transfer kinetics is determined in the simulations to be governed by the structure and flexibility of the side chains. Together, experiments and theory indicate that the proton mobility is the main determinant of proton conductivity, critical for the performance of peptide-based devices.

Three Methods for Peptide Cyclization Via Lactamization

Lactamization is the key step in the synthesis of many compounds with macrocyclic structure. As the interest for these types of molecules grows in various fields such as drug discovery and nanomaterials, different methodologies to access them are being developed. Three different strategies to obtain cyclic peptides via lactamization are described in this chapter: solution-phase macrocyclization following solid-phase peptide synthesis (SPPS) of the linear precursor, SPPS and on-resin cyclization on the 2-chlorotrityl chloride (2-CTC) resin, and SPPS and on-resin cyclization by native chemical ligation on the amino-PEGA resin.

Macromolecular assembly and membrane activity of antimicrobial D,L-α-Cyclic peptides

Antimicrobial peptides are viewed as a promising alternative to conventional antibiotics, as their activity through membrane targeting makes them less prone to resistance development. Among them, antimicrobial D,L-α-cyclic peptides (CPs) have been proposed as an alternative, specially due to their cyclic nature and to the presence of D-α-amino acids that increases their resistance to proteases. In present work, second generation D,L-α-cyclic peptides with proven antimicrobial activity are shown to form complex macromolecular assemblies in the presence of membranes. We addressed the CPs:membrane interactions through a combination of experimental techniques (DSC and ATR-FTIR) with coarse-grained molecular dynamics (CG-MD) simulations, aiming at understanding their interactions, macromolecular assemblies and eventually unveil their mechanism of action. DSC shows that the interaction depends heavily on the negatively charge content of the membrane and on lipid/peptide ratio, suggesting different mechanisms for the different peptides and lipid systems. CG-MD proved that CPs can self-assemble at the lipid surface as nanotubes or micellar aggregates, depending on the peptide, in agreement with ATR-FTIR results. Finally, our results shed light into possible mechanisms of action of the peptides with pending hydrocarbon tail, namely membrane extensive segregation and/or membrane disintegration through the formation of disk-like lipid/peptide aggregates.

Synthesis, Characterization and Evaluation of Peptide Nanostructures for Biomedical Applications

There is a challenging need for the development of new alternative nanostructures that can allow the coupling and/or encapsulation of therapeutic/diagnostic molecules while reducing their toxicity and improving their circulation and in-vivo targeting. Among the new materials using natural building blocks, peptides have attracted significant interest because of their simple structure, relative chemical and physical stability, diversity of sequences and forms, their easy functionalization with (bio)molecules and the possibility of synthesizing them in large quantities. A number of them have the ability to self-assemble into nanotubes, -spheres, -vesicles or -rods under mild conditions, which opens up new applications in biology and nanomedicine due to their intrinsic biocompatibility and biodegradability as well as their surface chemical reactivity via amino- and carboxyl groups. In order to obtain nanostructures suitable for biomedical applications, the structure, size, shape and surface chemistry of these nanoplatforms must be optimized. These properties depend directly on the nature and sequence of the amino acids that constitute them. It is therefore essential to control the order in which the amino acids are introduced during the synthesis of short peptide chains and to evaluate their in-vitro and in-vivo physico-chemical properties before testing them for biomedical applications. This review therefore focuses on the synthesis, functionalization and characterization of peptide sequences that can self-assemble to form nanostructures. The synthesis in batch or with new continuous flow and microflow techniques will be described and compared in terms of amino acids sequence, purification processes, functionalization or encapsulation of targeting ligands, imaging probes as well as therapeutic molecules. Their chemical and biological characterization will be presented to evaluate their purity, toxicity, biocompatibility and biodistribution, and some therapeutic properties in vitro and in vivo. Finally, their main applications in the biomedical field will be presented so as to highlight their importance and advantages over classical nanostructures.

Transmembrane Self-Assembled Cyclic Peptide Nanotubes Based on α-Residues and Cyclic δ-Amino Acids: A Computational Study

Self-assembling cyclic peptide nanotubes have been shown to function as synthetic, integral transmembrane channels. The combination of natural and nonnatural aminoacids in the sequence of cyclic peptides enables the control not only of their outer surface but also of the inner cavity behavior and properties, affecting, for instance, their permeability to different molecules including water and ions. Here, a thorough computational study on a new class of self-assembling peptide motifs, in which δ-aminocycloalkanecarboxylic acids are alternated with natural α-amino acids, is presented. The presence of synthetic δ-residues creates hydrophobic regions in these α,δ-SCPNs, which makes them especially attractive for their potential implementation in the design of new drug or diagnostic agent carrier systems. Using molecular dynamics simulations, the behavior of water molecules, different ions (Li+, Na+, K+, Cs+, and Ca2+), and their correspondent counter Cl- anions is extensively investigated in the nanoconfined environment. The structure and dynamics are mutually combined in a diving immersion inside these transmembrane channels to discover a fascinating submarine nanoworld where star-shaped water channels guide the passage of cations and anions therethrough.

Recent advances in design and applications of biomimetic self-assembled peptide hydrogels for hard tissue regeneration

Abstract

The development of natural biomaterials applied for hard tissue repair and regeneration is of great importance, especially in societies with a large elderly population. Self-assembled peptide hydrogels are a new generation of biomaterials that provide excellent biocompatibility, tunable mechanical stability, injectability, trigger capability, lack of immunogenic reactions, and the ability to load cells and active pharmaceutical agents for tissue regeneration. Peptide-based hydrogels are ideal templates for the deposition of hydroxyapatite crystals, which can mimic the extracellular matrix. Thus, peptide-based hydrogels enhance hard tissue repair and regeneration compared to conventional methods. This review presents three major self-assembled peptide hydrogels with potential application for bone and dental tissue regeneration, including ionic self-complementary peptides, amphiphilic (surfactant-like) peptides, and triple-helix (collagen-like) peptides. Special attention is given to the main bioactive peptides, the role and importance of self-assembled peptide hydrogels, and a brief overview on molecular simulation of self-assembled peptide hydrogels applied for bone and dental tissue engineering and regeneration.

Graphic abstract

Tubular supramolecular alternating copolymers fabricated by cyclic peptide-polymer conjugates

Supramolecular copolymers are an emerging class of materials, which bring together different properties and functionalities of multiple components via noncovalent interactions. While it is widely acknowledged that the repeating unit sequence plays an essential role on the performance of these materials, mastering and tuning the supramolecular copolymer sequence is still an open challenge. To date, only statistical supramolecular copolymers have been reported using cyclic peptide-polymer conjugates as building blocks. To enrich the diversity of tubular supramolecular copolymers, we report here a strategy of controlling their sequences by introducing an extra complementary noncovalent interaction. Hence, two conjugates bearing one electron donor and one electron acceptor, respectively, are designed. The two conjugates can individually assemble into tubular supramolecular homopolymers driven by the multiple hydrogen bonding interactions between cyclic peptides. However, the complementary charge transfer interaction between the electron donor and acceptor makes each conjugate more favorable for complexing with its counterpart, resulting in an alternating sequence of the supramolecular copolymer. Following the same principle, more functional supramolecular alternating copolymers are expected to be designed and constructed via other complementary noncovalent interactions (electrostatic interactions, metal coordination interactions, and host-guest interactions, etc.).

From Folding to Assembly: Functional Supramolecular Architectures of Peptides Comprised of Non-Canonical Amino Acids

The engineering of biological molecules is the fundamental concept behind the design of complex materials with desirable functions. Over the last few decades, peptides and proteins have emerged as useful building blocks for well-defined nanostructures with controlled size and dimensions. Short peptides in particular have received much attention due to their inherent biocompatibility, lower synthetic cost, and ease of tunability. In addition to the diverse self-assembling properties of short peptides comprising coded amino acids and their emerging applications in nanotechnology, there is now growing interest in the properties of peptides composed of non-canonical amino acids. Such non-natural oligomers have been shown in recent years to form well-defined secondary structures similar to natural proteins, with the ability to self-assemble to generate a wide variety of nanostructures with excellent biostability. This review describes recent events in the development of supramolecular assemblies of peptides composed completely of non-coded amino acids and their hybrid analogues. Special attention is paid to understanding the supramolecular assemblies at the atomic level and to considering their potential applications in nanotechnology.

Construction and Piezoelectric Properties of a Single-Peptide Nanotube Composed of Cyclic β-peptides with Helical Peptides on the Side Chains

To develop nanopiezoelectronics, it is necessary to investigate the relationship between the sizes and piezoelectric properties of the material. Peptide nanotubes (PNTs) composed of cyclic β-peptides have been studied as leading candidates for nanopiezoelectric materials. The current drawback of PNTs is aggregation to form a PNT bundle structure due to strong dipole-dipole interactions between PNTs. Here, we report the construction and piezoelectric properties of single PNTs without nonspecific aggregation by side-chain modification of helical peptides. A cyclic tri-β-peptide with a helical peptide was prepared by multiple-step liquid-phase peptide synthesis and assembled into PNTs by the vapor diffusion method. These nanotubes were characterized by polarized light microscopy and Fourier transform infrared (FTIR) spectroscopy. Additionally, atomic force microscopy (AFM) topographic images showed nanotubes with a height of 4 nm, which corresponds to the diameter of a PNT on a gold-coated mica substrate, indicating that a single PNT was prepared successfully. The converted piezoelectric response of a single PNT was determined to be 1.39 ± 0.12 pm/V. This value was consistent with that of a PNT bundle, which reveals that the piezoelectricity of PNTs is induced by deformation of their cyclic skeletons and is independent of the bundled structure. This finding not only demonstrates a new molecular design strategy to construct these smallest piezoelectric biomaterials by controlling the supramolecular hierarchical structures but also provides insights into the correlation between molecular assembly morphology and size-dependent piezoelectric properties.

Attenuated total reflection-Fourier transform infrared spectroscopy: a tool to characterize antimicrobial cyclic peptide-membrane interactions

Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) has been used for the structural characterization of peptides and their interactions with membranes. Antimicrobial peptides (AMPs) are part of our immune system and widely studied in recent years. Many linear AMPs have been studied, but their cyclization was shown to enhance the peptide's activity. We have used cyclic peptides (CPs) of an even number of alternating D- and L-α-amino acids, an emerging class of potential AMPs. These CPs can adopt a flat-ring shape that can stack into an antiparallel structure, forming intermolecular hydrogen bonds between different units, creating a tubular β-sheet structure - self-assembled cyclic peptide nanotubes (SCPNs). To get the structural information on peptides in solution and/or in contact with membranes, Amide I and II absorptions are used as they can adopt frequency and shape band characteristics that are influenced by the strength of existing hydrogen bonds between the amide CO and NH involved in secondary structures such as helix, β-sheet or aperiodic structures. The combination of polarized lens with ATR-FTIR provides an important tool to study the orientation of peptides when interacting with lipid membranes as the information can be derived on the position relative to the membrane normal. This work shows how ATR-FTIR used together with polarized light was successfully used to characterize structurally two CPs (RSKSWPgKQ and RSKSWX^C10KQ) in solution and upon interaction with negatively charged membranes of DMPG, assessing the formation and orientation of tubular structures (SCPNs) that were shown to be enhanced by the presence of the lipid membrane.

Effect of Water Models on Transmembrane Self-Assembled Cyclic Peptide Nanotubes

Self-assembling cyclic peptide nanotubes can form nanopores when they are inserted in lipid bilayers, acting as ion and/or water permeable channels. In order to improve the versatility of these systems, it is possible to specifically design cyclic peptides with a combination of natural and non-natural amino acids, enabling the control of the nature of the inner cavity of the channels. Here, the behavior of two types of self-assembling peptide motifs, alternating α-amino acids with γ- or δ-aminocycloalkanecarboxylic acids, is studied via molecular dynamics (MD) simulations. The behavior of water molecules in nanopores is expected to affect the properties of these channels and therefore merits detailed examination. A number of water models commonly used in MD simulations have been validated by how well they reproduce bulk water properties. However, it is less clear how these water models behave in the nanoconfined condition inside a channel. The behavior of four different water models-TIP3P, TIP4P, TIP4P/2005, and OPC-are evaluated in MD simulations of self-assembled cyclic peptide nanotubes of distinct composition and diameter. The dynamic behavior of the water molecules and ions in these designed artificial channels depends subtly on the water model used. TIP3P water molecules move faster than those of TIP4P, TIP4P/2005, and OPC. This demeanor is clearly observed in the filling of the nanotube, in water diffusion within the pore, and in the number and stability of hydrogen bonds of the peptides with water. It was also shown that the water model influences the simulated ion flux through the nanotubes, with TIP3P producing the greatest ion flux. Additionally, the two more recent models, TIP4P/2005 and OPC, which are known to reproduce the experimental self-diffusion coefficient of bulk water quite well, exhibit very similar results under the nanoconfined conditions studied here. Because none of these models have been parametrized specifically for waters confined in peptide nanotubes, this study provides a point of reference for further validation.

Alpha helical surfactant-like peptides self-assemble into pH-dependent nanostructures

A designed surfactant-like peptide is shown, using a combination of cryogenic-transmission electron microscopy and small-angle X-ray scattering, to have remarkable pH-dependent self-assembly properties. Peptide Arg₃-Leu₁₂ (R₃L₁₂) forms a network of peptide nanotubes at pH 9 and below. These are associated with α-helical conformation in a "cross-α" nanotube structure, in which peptide dimers lie perpendicular to the nanotube axis, with arginine coated inner and outer nanotube walls. In contrast, this peptide forms decorated vesicular aggregates at higher pH values, close to the pK_a of the arginine residues. These structures are associated with a loss of α-helical order as detected through X-ray scattering, circular dichroism and FTIR spectroscopy, the latter technique also revealing a loss of ordering of leucine side chains. This suggests a proposed model for the decorated or patchy vesicular structures that comprises disordered peptide as the matrix of the membrane, with small domains of ordered peptide dimers forming the minority domains. We ascribe this to a lipid-raft like phase separation process, due to conformational disordering of the leucine hydrophobic chains. The observation of the self-assembly of a simple surfactant-like peptide into these types of nanostructure is remarkable, and peptide R₃L₁₂ shows unique pH-dependent morphological and conformational behaviour, with the potential for a range of future applications.

Interaction of cyclosporin A molecules with alkali and transition metal atoms on Cu(111)

The structure of a cyclic peptide with important biological functionalities, cyclosporin A (CsA), is investigated at the single molecule level. Its adsorption on Cu(111) under ultra-high vacuum is characterised with scanning tunnelling microscopy (STM) and density functional theory. With STM investigations, we demonstrate element specific on-surface coordination schemes of CsA with coadsorbed K, Co and Fe atoms. Thus, clear insights emerge in the behaviour of cyclic peptides at interfaces and their interactions with different metal atoms, providing control of the adsorption structure and assembly and paving the way for the integration of cyclic peptides in functional metal-organic nanostructures on surfaces.

Helical Nanofibers Formed by Palladium-Mediated Assembly of Organic Homochiral Macrocycles Containing Binaphthyl and Pyridyl Units

Herein, we report the synthesis and characterization of homochiral macrocycles, in which molecular rigidity, combined with the presence of multiple functional groups, allow for the assembly of helical nanostructures. 1,1'-bi-2-naphthol (Binol) units are used as robust chirality inducers, and pyridyl units embedded within the molecular frameworks allow the assembly, upon coordination with Pd(II) metal ions, of the macrocyclic building blocks. CD and NMR spectroscopies show the formation of ordered 1D assembly in solution. AFM studies indicate that the molecular systems are capable of forming nanoscale structures. The effective transfer of chiral information results in helical nanofibers, with lengths ranging from a few hundreds of nanometers to some micrometers. AFM line profiles reveal a helical longitudinal period of about 50 nm and a transverse width of 25 to 45 nm after deconvolution.

Temperature Replica Exchange Molecular Dynamics Simulations of Cyclic Peptide Conformation

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Efficient Artificial Light-Harvesting System Based on Supramolecular Peptide Nanotubes in Water

Artificial light-harvesting systems in aqueous media which mimic nature are of significant importance; however, they are often restrained by the solubility and the undesired aggregation-caused quenching effect of the hydrophobic chromophores. Here, we report a generalized strategy toward the construction of efficient artificial light-harvesting systems based on supramolecular peptide nanotubes in water. By molecularly aligning the hydrophobic chromophores along the nanotubes in a slipped manner, an artificial light-harvesting system with a two-step sequential Förster resonance energy transfer process is successfully fabricated, showing an energy transfer efficiency up to 95% and a remarkably high fluorescence quantum yield of 30%, along with high stability. Furthermore, the spectral emission could be continuously tuned from blue through green to orange, as well as outputted as a white light continuum with a fluorescence quantum yield of 29.9%. Our findings provide a versatile approach of designing efficient artificial light-harvesting systems and constructing highly emissive organic materials in aqueous media.

Two-Dimensional Coordination Networks from Cyclic Dipeptides

Peptide-based biomimetic nanostructures and metal-organic coordination networks on surfaces are two promising classes of hybrid materials which have been explored recently. However, despite the great versatility and structural variability of natural and synthetic peptides, the two directions have so far not been merged in fabrication of metal-organic coordination networks using peptides as building blocks. Here we demonstrate that cyclic peptides can be used as ligands to form highly ordered, two-dimensional, peptide-based metal-organic coordination networks. The networks are formed on a Au(111) surface through coadsorption of cyclic dialanine with Cu-adatoms under Ultra-High Vacuum (UHV) conditions. Scanning Tunneling Microscopy (STM) in combination with X-ray Photoelectron spectroscopy (XPS) has been utilized to characterize the network structures at submolecular resolution and expound the chemical changes involved in network coordination. The networks involve a motif of three cyclic dialanine molecules coordinating to a central Cu-adatom. Interestingly the networks expose pores functionalized by the side chain of the cyclic peptide, suggesting a general method to form functionalized porous metal-organic networks on surfaces.

Colorimetric detection of glucose based on the binding specificity of a synthetic cyclic peptide

A novel colorimetric sensing method for glucose was developed based on the catalytic activity of Au nanoparticles (NPs) and a synthetic cyclic peptide that specifically binds with glucose. It is the first time that a cyclic peptide was used as a recognition element for glucose sensing. In the absence of glucose, the monolayers of cyclic peptide on the Au NP surfaces interfered little with the adsorption of 4-nitrophenol, and the Au NPs catalyze the reduction of bright yellow 4-nitrophenol to colorless 4-aminophenol in the presence of NaBH4. Added glucose was preferentially bound by the cyclic peptides and impeded the adsorption of 4-nitrophenol. Therefore, the color of the solution presented varying shades of yellow depending on the concentration of glucose. The method had a short response time of 10 min and demonstrated a linear response over a range of glucose concentrations from 0.1 mM to 20 mM, with a lower limit of detection of 0.04 mM. Meanwhile, it also provided results readily observable by the naked eye. The method was successfully applied for the detection of glucose in spiked food samples (Chinese cabbage, pear, and wheat flour) and spiked rabbit blood, and a good recovery rate of 88.04-103.28% and 94.27-101.53% was obtained, respectively.

Peptide nanotubes self-assembled from leucine-rich alpha helical surfactant-like peptides

The designed arginine-rich surfactant-like peptide R₃L₁₂ (arginine₃-leucine₁₂) is shown to form a remarkable diversity of self-assembled nanostructures in aqueous solution, depending on pH, including nanotubes, mesh-like tubular networks in three-dimensions and square planar arrays in two-dimensions. These structures are built from α-helical antiparallel coiled-coil peptide dimers arranged perpendicular to the nanotube axis, in a "cross-α" nanotube structure. The aggregation behavior is rationalized based on the effects of dimensionality, and the balance of hydrophobic and electrostatic interactions. The nanotube and nanomesh structures display arginine at high density on their surfaces, which may be valuable for future applications.

Strategies for Fine-Tuning the Conformations of Cyclic Peptides

Cyclic peptides are promising scaffolds for drug development, attributable in part to their increased conformational order compared to linear peptides. However, when optimizing the target-binding or pharmacokinetic properties of cyclic peptides, it is frequently necessary to "fine-tune" their conformations, e.g., by imposing greater rigidity, by subtly altering certain side chain vectors, or by adjusting the global shape of the macrocycle. This review systematically examines the various types of structural modifications that can be made to cyclic peptides in order to achieve such conformational control.

Cyclic γ-Peptides With Transmembrane Water Channel Properties

Self-assembling peptides can be used to design new materials for medical and biological applications. Here we synthesized and characterized two novel cyclic γ-peptides (γ-CPs) with hydrophobic inner surfaces. The NMR and FT-IR studies confirmed that the CPs could self-assemble into parallel stacking structures via intermolecular H-bonds and π-π interactions. The morphologies of the self-assembly CPs showed bundles of nanotubes via transmission electron microscopy (TEM); these nanotubes form water channels to transport water across the lipid membrane. The properties of blocking the transport of protons like natural water channels showed that the hydrophobic inner surfaces are important in artificial transmembrane water channel designs. These studies also showed that water transport was a function of pore size and length of the assemblies.

Supramolecular polymer bottlebrushes

The field of supramolecular chemistry has long been known to generate complex materials of different sizes and shapes via the self-assembly of single or multiple low molar mass building blocks. Matching the complexity found in natural assemblies, however, remains a long-term challenge considering its precision in organizing large macromolecules into well-defined nanostructures. Nevertheless, the increasing understanding of supramolecular chemistry has paved the way to several attempts in arranging synthetic macromolecules into larger ordered structures based on non-covalent forces. This review is a first attempt to summarize the developments in this field, which focus mainly on the formation of one-dimensional, linear, cylindrical aggregates in solution with pendant polymer chains - therefore coined supramolecular polymer bottlebrushes in accordance with their covalent equivalents. Distinguishing by the different supramolecular driving forces, we first describe systems based on π-π interactions, which comprise, among others, the well-known perylene motif, but also the early attempts using cyclophanes. However, the majority of reported supramolecular polymer bottlebrushes are formed by hydrogen bonds as they can for example be found in linear and cyclic peptides, as well as so called sticker molecules containing multiple urea groups. Besides this overview on the reported motifs and their impact on the resulting morphology of the polymer nanostructures, we finally highlight the potential benefits of such non-covalent interactions and refer to promising future directions of this still mostly unrecognized field of supramolecular research.

Parallel Versus Antiparallel β-Sheet Structure in Cyclic Peptide Hybrids Containing γ- or δ-Cyclic Amino Acids

Cyclic peptides with disc-shaped structures have emerged as potent building blocks for the preparation of new biomaterials in fields ranging from biological to material science. In this work, we analyze in depth the self-assembling properties of a new type of cyclic peptides based on the alternation of α-residues and cyclic δ-amino acids (α,δ-CPs). To examine the preferred stacking properties adopted by cyclic peptides bearing this type of amino acids, we carried out a synergistic in vitro/in silico approximation by using simple dimeric models and then extended to nanotubes. Although these new cyclic peptides (α,δ-CPs) can interact either in a parallel or antiparallel fashion, our results confirm that although the parallel β-sheet is more stable, it can be switched to the antiparallel stacking by choosing residues that can establish favorable cross-strand interactions. Moreover, the subsequent comparison by using the same methodology but applied to α,γ-CPs models, up to the moment assumed as antiparallel-like d,l-α-CPs, led to unforeseen conclusions that put into question preliminary conjectures about these systems. Surprisingly, they tend to adopt a parallel β-sheet directed by the skeleton interactions. These results imply a change of paradigm with respect to cyclic peptide designs that should be considered for dimers and nanotubes.