Self-assembling α,γ-cyclic peptides that generate cavities with tunable properties

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.

Hierarchical Materials from High Information Content Macromolecular Building Blocks: Construction, Dynamic Interventions, and Prediction

Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature. Because hierarchy gives rise to unique properties and functions, many have sought inspiration from nature when designing and fabricating hierarchical matter. More and more, however, nature's own high-information content building blocks, proteins, peptides, and peptidomimetics, are being coopted to build hierarchy because the information that determines structure, function, and interfacial interactions can be readily encoded in these versatile macromolecules. Here, we take stock of recent progress in the rational design and characterization of hierarchical materials produced from high-information content blocks with a focus on stimuli-responsive and "smart" architectures. We also review advances in the use of computational simulations and data-driven predictions to shed light on how the side chain chemistry and conformational flexibility of macromolecular blocks drive the emergence of order and the acquisition of hierarchy and also on how ionic, solvent, and surface effects influence the outcomes of assembly. Continued progress in the above areas will ultimately usher in an era where an understanding of designed interactions, surface effects, and solution conditions can be harnessed to achieve predictive materials synthesis across scale and drive emergent phenomena in the self-assembly and reconfiguration of high-information content building blocks.

Advances in hybrid peptide-based self-assembly systems and their applications

Self-assembly of peptides demonstrates a great potential for designing highly ordered, finely tailored supramolecular arrangements enriched with high specificity, improved efficacy and biological activity. Along with natural peptides, hybrid peptide systems composed of natural and chemically diverse unnatural amino acids have been used in various fields, including drug delivery, wound healing, potent inhibition of diseases, and prevention of biomaterial related diseases to name a few. In this review, we provide a brief outline of various methods that have been utilized for obtaining fascinating structures that create an avenue to reproduce a range of functions resulting from these folds. An overview of different self-assembled structures as well as their applications will also be provided. We believe that this review is very relevant to the current scenario and will cover conformations of hybrid peptides and resulting self-assemblies from the late 20^th century through 2022. This review aims to be a comprehensive and reliable account of the hybrid peptide-based self-assembly owing to its enormous influence in understanding and mimicking biological processes.

Molecular Self-Assembly and Supramolecular Chemistry of Cyclic Peptides

This Review focuses on the establishment and development of self-assemblies governed by the supramolecular interactions between cyclic peptides. The Review first describes the type of cyclic peptides able to assemble into tubular structures to form supramolecular cyclic peptide nanotubes. A range of cyclic peptides have been identified to have such properties, including α-peptides, β-peptides, α,γ-peptides, and peptides based on δ- and ε-amino acids. The Review covers the design and functionalization of these cyclic peptides and expands to a recent advance in the design and application of these materials through their conjugation to polymer chains to generate cyclic peptide-polymer conjugates nanostructures. The Review, then, concentrates on the challenges in characterizing these systems and presents an overview of the various analytical and characterization techniques used to date. This overview concludes with a critical survey of the various applications of the nanomaterials obtained from supramolecular cyclic peptide nanotubes, with a focus on biological and medical applications, ranging from ion channels and membrane insertion to antibacterial materials, anticancer drug delivery, gene delivery, and antiviral applications.

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.

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.

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.

Competitive double-switched self-assembled cyclic peptide nanotubes: a dual internal and external control

"Intelligent" materials based on synthetic small molecules that become functional only under specific conditions provide new opportunities for developing regulated systems aimed at a large number of applications. For instance, biologically active supramolecular entities that are sensitive to environmental conditions, such as the presence of bacterial membranes, are extremely interesting in biomedicine. In this work, we have designed and investigated, using molecular dynamics simulations, a doubly modulable nanotube formed by the self-assembly of cyclic peptides sensitive to both the presence of a lipid membrane and the pH of the aqueous media. The cyclic peptides were designed to self-assemble into peptide nanotubes in the presence of a lipid bilayer and at low pH values. Under these conditions, the residual side chains point outside the cyclic peptides, being exposed to the lipid bilayer, and the inner groups (carboxylic acids) are protonated, thus allowing the permeation of water and preventing that of ions. Higher pH values are expected to create carboxylate groups at the lumen of the peptides, leading to the disassembly of the nanotube, the attraction and translocation of ions towards the hydrophobic core of the bilayer, and eventually killing the target malignant cells. Our results suggest that by introducing a second switch in a membrane sensitive system, it is possible to modulate its interaction with the lipid bilayer. This opens the door to new strategies for the preparation of antimicrobial peptides that interact at the membrane level.

New self-assembling peptide nanotubes of large diameter using δ-amino acids

Here we show that 4-aminocyclohexanecarboxylic acid is a rigid stretcher building block for the preparation of cyclic peptides that self-assemble to form peptide nanotubes with large diameter and hydrophobic pores. The hydrophobic properties of the resulting nanotubes provided by the two methylene groups per δ-residue allow the encapsulation of C60 moieties forming a new type of bionanopeapod structure.

Two one-dimensional arrays of naphthyl and anthryl groups along peptide nanotubes prepared from cyclic peptides comprising α- and β-amino acids

A novel cyclic hexapeptide composed of l-α-naphthylalanine, d-α-anthrylalanine, and four β-alanines (CP6) is synthesized and its molecular assembly into peptide nanotubes (PNTs) and the electronic properties arising from one-dimensional arrays of aromatic groups along the PNTs were investigated. CP6 with a combination of l- and d-α-amino acids is designed to self-assemble into PNTs with them stacking on top of each other under the constraint of maximizing the number of intermolecular hydrogen bonds between the cyclic peptides. Upon PNT formation, the respective side chains of l- and d-α-amino acids are aligned in line along the PNTs. The topological arrangement of the anthryl groups being in close proximity in the CP6 PNT is supported by higher photo-excited energy transfer, appearance of the induced Cotton effects, and the promoted photo-dimerization reaction upon PNT formation. AFM observations reveal that PNT bundles with diameters 5-15 nm are dielectric microcrystals having a piezoelectric coefficient of 2-6 pC N-1. Kelvin force microscopy observations show the generation of surface potentials over 100 mV owing to the one-dimensional array of the anthryl groups along PNTs. Incorporation of α-amino acids with opposite chirality into cyclic β-peptides is therefore an effective molecular design for the nano-architecture of PNTs displaying one-dimensional arrays of chromophores along PNTs.

Sensing, Transport and Other Potential Biomedical Applications of Pseudopeptides

Pseudopeptides are privileged synthetic molecules built from the designed combination of peptide-like and abiotic artificial moieties. Consequently, they are benefited from the advantages of both families of chemical structures: modular synthesis, chemical and functional diversity, tailored three-dimensional structure, usually high stability in biological media and low non-specific toxicity. Accordingly, in the last years, these compounds have been used for different biomedical applications, ranging from bio-sensing, ion transport, the molecular recognition of biologically relevant species, drug delivery or gene transfection. This review highlights a selection of the most remarkable and recent advances in this field.

Understanding the conformational analysis of gababutin based hybrid peptides

A new class of gababutin-based tetrapeptide shows a C₁₂/C₁₀ hydrogen-bonded hybrid turn.

Chiral Nanotubes

Organic nanotubes, as assembled nanospaces, in which to carry out host-guest chemistry, reversible binding of smaller species for transport, sensing, storage or chemical transformation purposes, are currently attracting substantial interest, both as biological ion channel mimics, or for addressing tailored material properties. Nature's materials and machinery are universally asymmetric, and, for chemical entities, controlled asymmetry comes from chirality. Together with carbon nanotubes, conformationally stable molecular building blocks and macrocycles have been used for the realization of organic nanotubes, by means of their assembly in the third dimension. In both cases, chiral properties have started to be fully exploited to date. In this paper, we review recent exciting developments in the synthesis and assembly of chiral nanotubes, and of their functional properties. This review will include examples of either molecule-based or macrocycle-based systems, and will try and rationalize the supramolecular interactions at play for the three-dimensional (3D) assembly of the nanoscale architectures.

cis-Platinum Complex Encapsulated in Self-Assembling Cyclic Peptide Dimers

A new cyclic peptide dimer that encapsulates cisplatin complexes in its internal cavity is described. The resulting complex showed cytotoxic activity at A2780 ovarian cancer cell lines independent of acquired platinum resistance.

Self-assembling Venturi-like peptide nanotubes

We describe the design and synthesis of self-assembling peptide nanotubes that have an internal filter area and whose length and internal diameters, at the entrance and in the constricted area, are precisely controlled.

Recent advances in controlling the internal and external properties of self-assembling cyclic peptide nanotubes and dimers

Tuning the internal and external properties of self-assembling cyclic peptide nanotubes.

Water-soluble pillar[5]arene induced the morphology transformation of self-assembled nanostructures and had further application in paraquat detection

Hex-4ClPBI can self-assemble into nanotubes in water, and the tubular structures can be transformed into nanoribbons and further vesicles by addition of H⁺ and further WP5.

Glucose derivatives substitution and cyclic peptide diameter effects on the stability of the self-assembled cyclic peptide nanotubes; a joint QM/MD study

Dynamical behavior and the stability of eighteen nanostructures composed of cyclic peptide (CP) with the general structure of the cyclo(CO(CH₂)_{n=4, 6, 10}COCyst), in the gas phase, water and chloroform were investigated during 50ns molecular dynamic (MD) simulations. CP dimers and cyclic peptide nanotubes (CPNTs) are more stable in chloroform than water and this stability is reversely correlated with the ring size of the CP units. Also the effect of glucose derivatives substitution, d-glucose (S1) and N-methyl-d-glucamine (S2), on the stability and other physicochemical properties of the CP dimers and CPNTs were evaluated. These substitutions increase the inner-subunits hydrogen bonds (H-bond) which in turn increase the stability of these structures. Moreover, the S2 substitution in comparison to the S1 makes dimers and CPNTs more stable. Gibbs free energy analysis based on the MM-PBSA and MM-GBSA calculations confirmed that substitutions affect the stability of the studied nanostructures, considerably and an increase in the length of the CPNT units reduces their stability. Quantum chemistry calculations on the dimer structures using the density functional theory (DFT) and DFT-D3 methods were performed. Based on the DFT-D3 calculations, it was revealed that the dispersion interactions play a key role in the dimerization process. The ring size increment, elevates the dispersion interaction energy which is accordance with the MD results. H-bond formation between the CO and NH groups of the CP units inside the dimers have been analyzed by using the quantum theory of atoms in molecules and natural bond orbital description. Finally, through these analyses, the electrostatic interaction between the mentioned groups have been evaluated.