Chirality Effects in Peptide Assembly Structures

Can Chirality Answer Whether We Are Alone?

Detecting biosignatures of life in extraterrestrial environments remains one of the primary objectives of scientific inquiry. Currently, both remote and direct detection methods are primarily aimed at identifying key molecular classes fundamental to terrestrial biology. However, a more universally applicable spectroscopic approach could involve searching for homochiral molecules. Thus, this perspective delves into the significance of homochirality as a critical factor in the origin of life. Without homochirality, the formation of self-recognizing and self-replicating complex molecules would be hindered. The various hypotheses concerning the origin of homochiral molecules have been explored and analyzed within this context. This perspective emphasizes the potential for discovering extraterrestrial microscopic life through the detection of homochiral molecules using chirodetecting methods such as chromatography and chiroptical spectroscopy or circular polarimetry as a promising remote technique. This discussion highlights the importance of homochirality in the broader search for life beyond Earth and underscores the need for innovative methodologies and instrumentation in astrobiological research. These techniques can be an effective method for detecting homochirality on future planetary missions.

Tailoring topology and bio-interactions of triazine frameworks

The construction of covalent organic frameworks with special geometery and optical properties is of high interest, due to their unique physicochemical and biological properties. In this work, we report on a new method for the construction of triazine frameworks with defined topologies using coordination chemistry. Ball milling and wet chemical reactions between cyanuric chloride and melamine were directed in spatial arrangements and opposite optical activity. Cobalt was used as a directing agent to drive reactions into special morphologies, optical properties and biological activity. The enantiorecognition ability of triazine frameworks that was manifested in their activities against bacteria, demonstrated a new way for the construction of materials with specific interactions at biointerfaces.

Divergent self-assembly propensity of enantiomeric phenylalanine amphiphiles that undergo pH-induced nanofiber-to-nanoglobule conversion

This study presents the pathway diversity in the self-assembly of enantiomeric single phenylalanine derived amphiphiles (single F-PDAs), viz.L-NapF-EDA and D-NapF-EDA, that form supramolecular hydrogels at varied concentrations (≥1 mg mL-1 and ≥3 mg mL-1, respectively). By fitting the variable temperature circular dichroism (VT-CD) data to the isodesmic model, various thermodynamic parameters associated with their self-assembly, such as association constant (K), changes in enthalpy (ΔH), entropy (ΔS), and Gibbs free energy (ΔG), were extracted. The self-assembly of these single F-PDAs was found to be enthalpy-driven but entropically-disfavored. Although self-assembly of the D-isomer was slow, it also exhibited greater free energy of association than the L-isomer. Consequently, thermally and mechanically more robust self-assemblies were formed by the D-isomer than the L-isomer. We term these results as the "butterfly effect in self-assembly" wherein the difference in the stereochemical orientation of the residues at a single chiral center present in these molecules resulted in strong differences in the self-assembly propensity as well as in their thermal and mechanical stability. These single F-PDAs form helical nanofibers of opposite chirality upon self-assembly at basic pH (≥8) that produce intense CD signals. However, upon decreasing the pH, a gradual nanofiber-to-nanoglobular transformation was noticed due to protonation-induced structural changes in the PDAs.

Biostable hydrogels consisting of hybrid β-sheet fibrils assembled by a pair of enantiomeric peptides

The assembly of chiral peptides facilitates the formation of diverse supramolecular structures with unique physicochemical and biological properties. However, the effects of chirality on peptide assembly and resulting hydrogel properties remain underexplored. In this study, we systematically investigated the assembly propensity, morphology, and biostability of mixture of a pair of enantiomeric peptides LELCLALFLF (ECF-5) and DEDCDADFDF (ecf-5) at various ratios. Results indicate the development of β-sheet fibrils, ultimately leading to the formation of self-supporting hybrid hydrogels. The hydrogel formed at a ratio of 1:1 exhibits a significantly lower storage modulus (G') than of the ratios of 0:1, 1:3, 3:1 and 1:0 (nD/nL; same below). Kink-separated fragments of approximately 100 nm in length predominate at ratios of 1:3 and 3:1, compared with the smooth fibrils at other ratios, probably attributed to an alternating arrangement of the co-assembled and self-assembled peptide fragments. The introduction of ecf-5 to the hybrid hydrogels improves resistance to proteolytic digestion and maintains commendable biocompatibility in both MIN6 and HUVECs cells. These findings provide valuable insights into the development of hydrogels with tailored properties, positing them potential scaffolds for 3D cell culture and tissue engineering.

Self-assembling peptides: Perspectives regarding biotechnological applications and vaccine development

Self-assembly involves a set of molecules spontaneously interacting in a highly coordinated and dynamic manner to form a specific supramolecular structure having new and clearly defined properties. Many examples of this occur in nature and many more came from research laboratories, with their number increasing every day via ongoing research concerning complex biomolecules and the possibility of harnessing it when developing new applications. As a phenomenon, self-assembly has been described on very different types of molecules (biomolecules including), so this review focuses on what is known about peptide self-assembly, its origins, the forces behind it, how the properties of the resulting material can be tuned in relation to experimental considerations, some biotechnological applications (in which the main protagonists are peptide sequences capable of self-assembly) and what is yet to be tuned regarding their research and development.

Topoisomeric Membrane-Active Peptides: A Review of the Last Two Decades

In recent decades, bioactive peptides have been gaining recognition in various biomedical areas, such as intracellular drug delivery (cell-penetrating peptides, CPPs) or anti-infective action (antimicrobial peptides, AMPs), closely associated to their distinct mode of interaction with biological membranes. Exploiting the interaction of membrane-active peptides with diverse targets (healthy, tumoral, bacterial or parasitic cell membranes) is opening encouraging prospects for peptides in therapeutics. However, ordinary peptides formed by L-amino acids are easily decomposed by proteases in biological fluids. One way to sidestep this limitation is to use topoisomers, namely versions of the peptide made up of D-amino acids in either canonic (enantio) or inverted (retroenantio) sequence. Rearranging peptide sequences in this fashion provides a certain degree of native structure mimicry that, in appropriate contexts, may deliver desirable biological activity while avoiding protease degradation. In this review, we will focus on recent accounts of membrane-active topoisomeric peptides with therapeutic applications as CPP drug delivery vectors, or as antimicrobial and anticancer candidates. We will also discuss the most common modes of interaction of these peptides with their membrane targets.

Impact of Non-Covalent Interactions of Chiral Linked Systems in Solution on Photoinduced Electron Transfer Efficiency

It is well-known that non-covalent interactions play an essential role in the functioning of biomolecules in living organisms. The significant attention of researchers is focused on the mechanisms of associates formation and the role of the chiral configuration of proteins, peptides, and amino acids in the association. We have recently demonstrated the unique sensitivity of chemically induced dynamic nuclear polarization (CIDNP) formed in photoinduced electron transfer (PET) in chiral donor-acceptor dyads to non-covalent interactions of its diastereomers in solutions. The present study further develops the approach for quantitatively analyzing the factors that determine the association by examples of dimerization of the diastereomers with the RS, SR, and SS optical configurations. It has been shown that, under the UV irradiation of dyads, CIDNP is formed in associates, namely, homodimers (SS-SS), (SR-SR), and heterodimers (SS-SR) of diastereomers. In particular, the efficiency of PET in homo-, heterodimers, and monomers of dyads completely determines the forms of dependences of the CIDNP enhancement coefficient ratio of SS and RS, SR configurations on the ratio of diastereomer concentrations. We expect that the use of such a correlation can be useful in identifying small-sized associates in peptides, which is still a problem.

Strategic Approaches to Improvise Peptide Drugs as Next Generation Therapeutics

In recent years, the occurrence of a wide variety of drug-resistant diseases has led to an increase in interest in alternate therapies. Peptide-based drugs as an alternate therapy hold researchers' attention in various therapeutic fields such as neurology, dermatology, oncology, metabolic diseases, etc. Previously, they had been overlooked by pharmaceutical companies due to certain limitations such as proteolytic degradation, poor membrane permeability, low oral bioavailability, shorter half-life, and poor target specificity. Over the last two decades, these limitations have been countered by introducing various modification strategies such as backbone and side-chain modifications, amino acid substitution, etc. which improve their functionality. This has led to a substantial interest of researchers and pharmaceutical companies, moving the next generation of these therapeutics from fundamental research to the market. Various chemical and computational approaches are aiding the production of more stable and long-lasting peptides guiding the formulation of novel and advanced therapeutic agents. However, there is not a single article that talks about various peptide design approaches i.e., in-silico and in-vitro along with their applications and strategies to improve their efficacy. In this review, we try to bring different aspects of peptide-based therapeutics under one article with a clear focus to cover the missing links in the literature. This review draws emphasis on various in-silico approaches and modification-based peptide design strategies. It also highlights the recent progress made in peptide delivery methods important for their enhanced clinical efficacy. The article would provide a bird's-eye view to researchers aiming to develop peptides with therapeutic applications.

Graphical Abstract

Laser-Induced Chirality of Plasmonic Nanoparticles Embedded in Porous Matrix

Chiral plasmonic nanostructures have emerged as promising objects for numerous applications in nanophotonics, optoelectronics, biosensing, chemistry, and pharmacy. Here, we propose a novel method to induce strong chirality in achiral ensembles of gold nanoparticles via irradiation with circularly-polarized light of a picosecond Nd:YAG laser. Embedding of gold nanoparticles into a nanoporous silicate matrix leads to the formation of a racemic mixture of metal nanoparticles of different chirality that is enhanced by highly asymmetric dielectric environment of the nanoporous matrix. Then, illumination with intense circularly-polarized light selectively modifies the particles with the chirality defined by the handedness of the laser light, while their "enantiomers" survive the laser action almost unaffected. This novel modification of the spectral hole burning technique leads to the formation of an ensemble of plasmonic metal nanoparticles that demonstrates circular dichroism up to 100 mdeg. An unforeseen peculiarity of the chiral nanostructures obtained in this way is that 2D and 3D nanostructures contribute almost equally to the observed circular dichroism signals. Thus, the circular dichroism is neither even nor odd under reversal of direction of light propagation. These findings will help guide the development of a passive optical modulator and nanoplatform for enhanced chiral sensing and catalysis.

Identification of heterochirality-mediated stereochemical interactions in peptide architectures

In this work, we illustrate a strategy for constructing heterochiral peptide architectures with distinct structural, mechanical and thermal characteristics. A series of nanotube structures based on diphenylalanine (FF) and its chiral derivatives were examined. Pronounced effects relating to heterochirality on mechanostability and thermal stability can be identified. The homochiral peptide FF and its enantiomer ff formed nanotubes with high thermal and mechanical stabilities (Young's modulus: 20.3 ± 5.9 GPa for FF and 21.2 ± 4.7 GPa for ff). In contrast, heterochiral nanotubes formed by Ff and fF manifest superstructures along the axial direction with differed thermal and mechanical strength (Young's modulus: 7.3 ± 2.4 GPa for Ff and 8.3 ± 2.1 GPa for fF). Combining their single-crystal XRD structure and in silico results, it was demonstrated that the spatial orientations of aromatic moieties were subtly changed by heterochirality of peptide building blocks, which led to intramolecular face-to-face interactions. As the result, both intermolecular axial and interchannel interactions in heterochiral nanotubes were weakened as reflected in the strikingly deteriorated mechanical and thermal stabilities. Conversely, two aromatic side chains of the homochiral peptides were staggered and formed interdigitated steric zippers, which served as strong glues that secured the robustness of nanotubes in both axial and radial orientation. Furthermore, the generality of the heterochiral-mediated stereochemical effects was demonstrated in other "FF class" dipeptides, including fluorinated Ff, FW and FL. Our results unequivocally revealed the relationship between amino acid chirality, peptide molecule packing, and physical stabilities of "FF class" dipeptide self-assembled materials and provide valuable molecular insights into chirality-mediated stereochemical interactions in determining the properties of peptide architectures.

Photoinduced Processes in Lysine-Tryptophan-Lysine Tripeptide with L and D Tryptophan

Optical isomers of short peptide Lysine-Tryptophan-Lysine (Lys-{L/D-Trp}-Lys) and Lys-Trp-Lys with an acetate counter-ion were used to study photoinduced intramolecular and intermolecular processes of interest in photobiology. A comparison of L- and D-amino acid reactivity is also the focus of scientists' attention in various specialties because today, the presence of amyloid proteins with D-amino acids in the human brain is considered one of the leading causes of Alzheimer's disease. Since aggregated amyloids, mainly Aβ42, are highly disordered peptides that cannot be studied with traditional NMR and X-ray techniques, it is trending to explore the reasons for differences between L- and D-amino acids using short peptides, as in our article. Using NMR, chemically induced dynamic nuclear polarization (CIDNP) and fluorescence techniques allowed us to detect the influence of tryptophan (Trp) optical configuration on the peptides fluorescence quantum yields, bimolecular quenching rates of Trp excited state, and the photocleavage products formation. Thus, compared with the D-analog, the L-isomer shows a greater Trp excited state quenching efficiency with the electron transfer (ET) mechanism. There are experimental confirmations of the hypothesis about photoinduced ET between Trp and the CONH peptide bond, as well as between Trp and another amide group.

Peptide Carbocycles: From -SS- to -CC- via a Late-Stage "Snip-and-Stitch"

One way to improve the therapeutic potential of peptides is through cyclization. This is commonly done using a disulfide bond between two cysteine residues in the peptide. However, disulfide bonds are susceptible to reductive cleavage, and this can deactivate the peptide and endanger endogenous proteins through covalent modification. Substituting disulfide bonds with more chemically robust carbon-based linkers has proven to be an effective strategy to better develop cyclic peptides as drugs, but finding the optimal carbon replacement is synthetically laborious. We report a new late-stage platform wherein a single disulfide bond in a cyclic peptide can serve as the progenitor for any number of new carbon-rich groups, derived from organodiiodides, using a Zn:Cu couple and a hydrosilane. We show that this platform can furnish entirely new carbocyclic scaffolds with enhanced permeability and structural integrity and that the stereochemistry of the new cycles can be biased by a judicious choice in silane.

Peptide-Based Low Molecular Weight Photosensitive Supramolecular Gelators

Over the last couple of decades, stimuli-responsive supramolecular gels comprising synthetic short peptides as building blocks have been explored for various biological and material applications. Though a wide range of stimuli has been tested depending on the structure of the peptides, light as a stimulus has attracted extensive attention due to its non-invasive, non-contaminant, and remotely controllable nature, precise spatial and temporal resolution, and wavelength tunability. The integration of molecular photo-switch and low-molecular-weight synthetic peptides may thus provide access to supramolecular self-assembled systems, notably supramolecular gels, which may be used to create dynamic, light-responsive “smart” materials with a variety of structures and functions. This short review summarizes the recent advancement in the area of light-sensitive peptide gelation. At first, a glimpse of commonly used molecular photo-switches is given, followed by a detailed description of their incorporation into peptide sequences to design light-responsive peptide gels and the mechanism of their action. Finally, the challenges and future perspectives for developing next-generation photo-responsive gels and materials are outlined.

Molecular Dynamics Simulation Study of the Self-Assembly of Phenylalanine Peptide Nanotubes

In this paper, we propose and use a new approach for a relatively simple technique for conducting MD simulation (MDS) of various molecular nanostructures, determining the trajectory of the MD run and forming the final structure using external force actions. A molecular dynamics manipulator (MD manipulator) is a controlled MDS type. As an example, the applicability of the developed algorithm for assembling peptide nanotubes (PNT) from linear phenylalanine (F or Phe) chains of different chirality is presented. The most adequate regimes for the formation of nanotubes of right chirality D from the initial L-F and nanotubes of left chirality L of their initial dipeptides D-F modes were determined. We use the method of a mixed (vector–scalar) product of the vectors of the sequence of dipole moments of phenylalanine molecules located along the nanotube helix to calculate the magnitude and sign of chirality of self-assembled helical phenylalanine nanotubes, which shows the validity of the proposed approach. As result, all data obtained correspond to the regularity of the chirality sign change of the molecular structures with a hierarchical complication of their organization.

Quantitative Assessment of Chirality of Protein Secondary Structures and Phenylalanine Peptide Nanotubes

In this study we consider the features of spatial-structure formation in proteins and their application in bioengineering. Methods for the quantitative assessment of the chirality of regular helical and irregular structures of proteins are presented. The features of self-assembly of phenylalanine (F) into peptide nanotubes (PNT), which form helices of different chirality, are also analyzed. A method is proposed for calculating the magnitude and sign of the chirality of helix-like peptide nanotubes using a sequence of vectors for the dipole moments of individual peptides.

Mitochondria-Targeted Self-Assembly of Peptide-Based Nanomaterials

Mitochondria are well known to serve as the powerhouse for cells and also the initiator for some vital signaling pathways. A variety of diseases are discovered to be associated with the abnormalities of mitochondria, including cancers. Thus, targeting mitochondria and their metabolisms are recognized to be promising for cancer therapy. In recent years, great efforts have been devoted to developing mitochondria-targeted pharmaceuticals, including small molecular drugs, peptides, proteins, and genes, with several molecular drugs and peptides enrolled in clinical trials. Along with the advances of nanotechnology, self-assembled peptide-nanomaterials that integrate the biomarker-targeting, stimuli-response, self-assembly, and therapeutic effect, have been attracted increasing interest in the fields of biotechnology and nanomedicine. Particularly, in situ mitochondria-targeted self-assembling peptides that can assemble on the surface or inside mitochondria have opened another dimension for the mitochondria-targeted cancer therapy. Here, we highlight the recent progress of mitochondria-targeted peptide-nanomaterials, especially those in situ self-assembly systems in mitochondria, and their applications in cancer treatments.

Modeling of Self-Assembled Peptide Nanotubes and Determination of Their Chirality Sign Based on Dipole Moment Calculations

The chirality quantification is of great importance in structural biology, where the differences in proteins twisting can provide essentially different physiological effects. However, this aspect of the chirality is still poorly studied for helix-like supramolecular structures. In this work, a method for chirality quantification based on the calculation of scalar triple products of dipole moments is suggested. As a model structure, self-assembled nanotubes of diphenylalanine (FF) made of L- and D-enantiomers were considered. The dipole moments of FF molecules were calculated using semi-empirical quantum-chemical method PM3 and the Amber force field method. The obtained results do not depend on the used simulation and calculation method, and show that the D-FF nanotubes are twisted tighter than L-FF. Moreover, the type of chirality of the helix-like nanotube is opposite to that of the initial individual molecule that is in line with the chirality alternation rule general for different levels of hierarchical organization of molecular systems. The proposed method can be applied to study other helix-like supramolecular structures.