The Phe-Phe Motif for Peptide Self-Assembly in Nanomedicine

Regulating H2S release from self-assembled peptide H2S-donor conjugates using cysteine derivatives

Self-assembled peptides provide a modular and diverse platform for drug delivery, and innovative delivery methods are needed for delivery of hydrogen sulfide (H2S), an endogenous signaling molecule (gasotransmitter) with significant therapeutic potential. Of the available types of H2S donors, peptide/protein H2S donor conjugates (PHDCs) offer significant versatility. Here we discuss the design, synthesis, and in-depth study of a PHDC containing three covalently linked components: a thiol-triggered H2S donor based on an S-aroylthiooxime (SATO), a GFFF tetrapeptide, and a tetraethylene glycol (TEG) dendron. Conventional transmission electron microscopy showed that the PHDC self-assembled into spherical structures without heat or stirring, but it formed nanofibers with gentle heat (37 °C) and stirring. Circular dichroism (CD) spectroscopy data collected during self-assembly under nanofiber-forming conditions suggested an increase in β-sheet character and a decrease in organization of the SATO units. Release of H2S from the nanofibers was studied through triggering with various thiols. The release rate and total amount of H2S released over both short (5 h) and long (7 d) time scales varied with the charge state: negatively charged and zwitterionic thiols (e.g., Ac-Cys-OH and H-Cys-OH) triggered release slowly while a neutral thiol (Ac-Cys-OMe) showed ∼10-fold faster release, and a positively charged thiol (H-Cys-OMe) triggered H2S release nearly 50-fold faster than the negatively charged thiols. CD spectroscopy studies monitoring changes in secondary structure over time during H2S release showed similar trends. This study sheds light on the driving forces behind self-assembling nanostructures and offers insights into tuning H2S release through thiol charge state modulation.

A Journey of Challenges and Victories: A Bibliometric Worldview of Nanomedicine since the 21st Century

Nanotechnology profoundly affects the advancement of medicine. Limitations in diagnosing and treating cancer and chronic diseases promote the growth of nanomedicine. However, there are very few analytical and descriptive studies regarding the trajectory of nanomedicine, key research powers, present research landscape, focal investigative points, and future outlooks. Herein, articles and reviews published in the Science Citation Index Expanded of Web of Science Core Collection from first January 2000 to 18th July 2023 are analyzed. Herein, a bibliometric visualization of publication trends, countries/regions, institutions, journals, research categories, themes, references, and keywords is produced and elaborated. Nanomedicine-related academic output is increasing since the COVID-19 pandemic, solidifying the uneven global distribution of research performance. While China leads in terms of publication quantity and has numerous highly productive institutions, the USA has advantages in academic impact, commercialization, and industrial value. Nanomedicine integrates with other disciplines, establishing interdisciplinary platforms, in which drug delivery and nanoparticles remain focal points. Current research focuses on integrating nanomedicine and cell ferroptosis induction in cancer immunotherapy. The keyword "burst testing" identifies promising research directions, including immunogenic cell death, chemodynamic therapy, tumor microenvironment, immunotherapy, and extracellular vesicles. The prospects, major challenges, and barriers to addressing these directions are discussed.

Divalent metal ion modulation of a simple peptide-based hydrogel: self-assembly and viscoelastic properties

Peptide self-assembly has been highly studied to understand the pathways in forming higher order structures along with the development and application of resulting hydrogel materials. Driven by noncovalent interactions, peptide hydrogels are stimuli-responsive to any addition to its gelling conditions. Here, a Phe-His based peptide, C14-FH(Trt)-OH, was synthesized and characterized with 1H NMR, FT-IR, MS, UV-vis spectroscopies and elemental analysis. Based on SEM imaging, the dipeptide conjugate was capable of forming a nanofibrous, interconnected network encapsulating buffer to produce a supramolecular hydrogel. Through the addition of Zn2+ and Cu2+, there is a clear change in the self-assembled nanostructures characterized through SEM. With this effect on self-assembly follows a change in the viscoelastic properties of the material, as determined through rheological frequency sweeps, with 2 and 3 orders of magnitude decreases in the elastic modulus G' in the presence of Zn2+ and Cu2+ respectively. This highlights the tunability of soft material properties with peptide design and self-assembly, through metal ions and Nδ-directed coordination.

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.

Self-Assembled Materials Based on Fully Aromatic Peptides: The Impact of Tryptophan, Tyrosine, and Dopa Residues

Peptides are able to self-organize in structural elements including cross-β structures. Taking advantage of this tendency, in the last decades, peptides have been scrutinized as molecular elements for the development of multivalent supramolecular architectures. In this context, different classes of peptides, also with completely aromatic sequences, were proposed. Our previous studies highlighted that the (FY)3 peptide, which alternates hydrophobic phenylalanine and more hydrophilic tyrosine residues, is able to self-assemble, thanks to the formation of both polar and apolar interfaces. It was observed that the replacement of Phe and Tyr residues with other noncoded aromatic amino acids like 2-naphthylalanine (Nal) and Dopa affects the interactions among peptides with consequences on the supramolecular organization. Herein, we have investigated the self-assembling behavior of two novel (FY)3 analogues with Trp and Dopa residues in place of the Phe and Tyr ones, respectively. Additionally, PEGylation of the N-terminus was analyzed too. The supramolecular organization, morphology, and capability to gel were evaluated using complementary techniques, including fluorescence, Fourier transform infrared spectroscopy, and scanning electron microscopy. Structural periodicities along and perpendicular to the fiber axis were detected by grazing incidence wide-angle X-ray scattering. Finally, molecular dynamics studies provided interesting insights into the atomic structure of the cross-β that constitutes the basic motif of the assemblies formed by these novel peptide systems.

Solvent-Induced Transient Self-Assembly of Peptide Gels: Gelator-Solvent Reactions and Material Properties Correlation

Herein, we introduce a new methodology for designing transient organogels that offers tunability of the mechanical properties simply by matching the protective groups of the precursor to that of the solvent. We developed solvent-induced transient materials in which the solvent chemically participates in a set of reactions and actively supports the assembly event. The activation of a single precursor by an acid (accelerator) yields the formation of two distinct gelators and induces gelation. The interconversion cycle is supplied by the secondary solvent (originating from hydrolysis of the primary solvent by the accelerator), which then progressively solubilizes the gel network. We show that this gelation method offers a direct correlation between the mechanical and transient properties by modifying the chemical structure of the precursors and the presence of an accelerator in the system. Such a method paves the way for the design of self-abolishing and mechanically tunable materials for targeted purposes. The biocompatibility and versatility of amino acid-based gelators can offer a wide range of biomaterials for applications requiring a controllable and definite lifetime such as drug delivery platforms exhibiting a burst release or self-abolishing cell culture substrates.

Dancing with Nucleobases: Unveiling the Self-Assembly Properties of DNA and RNA Base-Containing Molecules for Gel Formation

Nucleobase-containing molecules are compounds essential in biology due to the fundamental role of nucleic acids and, in particular, G-quadruplex DNA and RNA in life. Moreover, some molecules different from nucleic acids isolated from different vegetal sources or microorganisms show nucleobase moieties in their structure. Nucleoamino acids and peptidyl nucleosides belong to this molecular class. Closely related to the above, nucleopeptides, also known as nucleobase-bearing peptides, are chimeric derivatives of synthetic origin and more rarely isolated from plants. Herein, the self-assembly properties of a vast number of structures, belonging to the nucleic acid and nucleoamino acid/nucleopeptide family, are explored in light of the recent scientific literature. Moreover, several technologically relevant properties, such as the hydrogelation ability of some of the nucleobase-containing derivatives, are reviewed in order to make way for future experimental investigations of newly devised nucleobase-driven hydrogels. Nucleobase-containing molecules, such as mononucleosides, DNA, RNA, quadruplex (G4)-forming oligonucleotides, and nucleopeptides are paramount in gel and hydrogel formation owing to their distinctive molecular attributes and ability to self-assemble in biomolecular nanosystems with the most diverse applications in different fields of biomedicine and nanotechnology. In fact, these molecules and their gels present numerous advantages, underscoring their significance and applicability in both material science and biomedicine. Their versatility, capability for molecular recognition, responsiveness to stimuli, biocompatibility, and biodegradability collectively contribute to their prominence in modern nanotechnology and biomedicine. In this review, we emphasize the critical role of nucleobase-containing molecules of different nature in pioneering novel materials with multifaceted applications, highlighting their potential in therapy, diagnostics, and new nanomaterials fabrication as required for addressing numerous current biomedical and nanotechnological challenges.

Phenylalanine-based fibrillar systems

Phenylketonuria (PKU) is an inborn metabolic disorder characterized by excess accumulation of phenylalanine (Phe) and its fibril formation, resulting in progressive intellectual disability. Several research groups have approached from various directions to understand the formation of toxic amyloid fibrils from the essential amino acid Phe. Different parameters like the nature of the solvent, pH, Phe concentration, temperature, etc. influence the fibril formation kinetics. In this article, we have summarized all major findings regarding the formation of Phe-based fibrils in aqueous and organic media and discussed how non-covalent interactions are involved in the self-assembly process using spectroscopic and microscopic techniques. The toxicity of Phe-based fibrils is compared with other neurodegenerative peptides. It is noted that the Phe-based fibrils can also induce various globular proteins into toxic fibrils. Later, we discuss the different approaches to inhibit fibril formation and reduce its toxicity. The presence of polyphenolic compounds, drugs, amino acids, nanoparticles, metal ions, crown ethers, and others showed a remarkable inhibitory effect on fibril formation. To the best of our knowledge, this is the first-ever etymological analysis of the Phe-fibrillar system and its inhibition to create a strong database against PKU.

Transparent Organogels as a Medium for the Light-Induced Conversion from Spiropyran to Merocyanine

Low-molecular-weight peptide gelators are a versatile class of compounds able to form gels under a variety of conditions, even via simple ultrasound sonication. In this paper, the ability of Boc-L-Phe-D-Oxd-L-Phe-OBn to gelate three organic solvents (toluene, tert-butyl methyl ether, and ethanol) was evaluated. The rheological behaviour of the materials was assessed via strain sweep analysis, while the fibrous network was analysed via optical microscopy on the wet gels. The gel obtained from toluene is a highly transparent material, and the one from ethanol appears translucent, while the one from tert-butyl methyl ether is opaque. These gels were used to study the reversible light-induced transformation from spyropiran (SP) to merocyanine (MC) and back, as a model system to check the effect of the gel medium onto the rection kinetic. We observed that the solvent used to form the organogels has a crucial effect on the reaction, as gels from aprotic solvents stabilize the SP form, while the ones from protic solvents stabilize the MC form. We thus obtained a solid support to stabilize the two photochromic species just by changing the solvent polarity. Moreover, we could demonstrate that the self-assembled gels do not interfere with the light-driven conversion process, either starting from SP or MC, thus representing a valid and economical photochromic material.

Histidine modulates amyloid-like assembly of peptide nanomaterials and confers enzyme-like activity

Amyloid-like assembly is not only associated with pathological events, but also leads to the development of novel nanomaterials with unique properties. Herein, using Fmoc diphenylalanine peptide (Fmoc-F-F) as a minimalistic model, we found that histidine can modulate the assembly behavior of Fmoc-F-F and induce enzyme-like catalysis. Specifically, the presence of histidine rearranges the β structure of Fmoc-F-F to assemble nanofilaments, resulting in the formation of active site to mimic peroxidase-like activity that catalyzes ROS generation. A similar catalytic property is also observed in Aβ assembled filaments, which is correlated with the spatial proximity between intermolecular histidine and F-F. Notably, the assembled Aβ filaments are able to induce cellular ROS elevation and damage neuron cells, providing an insight into the pathological relationship between Aβ aggregation and Alzheimer's disease. These findings highlight the potential of histidine as a modulator in amyloid-like assembly of peptide nanomaterials exerting enzyme-like catalysis.

Short Peptides for Hydrolase Supramolecular Mimicry and Their Potential Applications

Hydrolases are enzymes that have found numerous applications in various industrial sectors spanning from pharmaceuticals to foodstuff and beverages, consumers' products such as detergents and personal care, textiles, and even for biodiesel production and environmental bioremediation. Self-assembling and gelling short peptides have been designed for their mimicry so that their supramolecular organization leads to the creation of hydrophobic pockets for catalysis to occur. Catalytic gels of this kind can also find numerous industrial applications to address important global challenges of our time. This concise review focuses on the last 5 years of progress in this fast-paced, popular field of research with an eye towards the future.

Influence of pH on the self-assembly of diphenylalanine peptides: molecular insights from coarse-grained simulations

Nanostructures fabricated from peptide self-assemblies are attracting increasing attention owing to their possible applications in biology and nanotechnology. A known example is an aromatic dipeptide (diphenylalanine, FF) which is extracted from Alzheimer's β-amyloid polypeptide as the core recognition motif for molecular self-assembly. Many studies have been carried out to organize FF peptides into various functional ordered nanostructures. For potential applications of self-assembled FF-based nanomaterials, it becomes important to consider some influencing factors (e.g., solvents, peptide concentrations, pH, temperature, etc.) on the self-assembly process. Among these factors, the effect of pH on the self-assembly process of FF peptides into assembled nanostructures through simulation studies is the main focus of the present work. In the current study, we have investigated the assembly pathway of 1000 FF peptides and qualitatively evaluated the morphological changes of FF-based nanostructures at different pH values by performing extensive coarse-grained molecular dynamics (CG-MD) simulations. Structural analyses suggest that FF peptides can spontaneously assemble into nanotubes with different shapes under acidic, neutral and basic conditions. Based on the analysis of FF nanostructure formation pathways in different pH solutions, the self-assembly of the nanotube involves the aggregation of molecules to form a bilayer, the curling of a bilayer to form a vesicle and the transformation of a vesicle into a tubular structure. It is noted that a flat hollow columnar structure is observed as a special intermediate state during the transformation process of a vesicle-like to a tube-like structure. Energetic analysis suggests that the aggregation of FF peptides is driven by the vdW interactions but the aggregation shape is mainly affected by the electrostatic interactions. Overall, this study provides further understanding of the self-assembly behavior of aromatic short peptide derivatives in different pH solutions.

Advancements in Biosensors Based on the Assembles of Small Organic Molecules and Peptides

Over the past few decades, molecular self-assembly has witnessed tremendous progress in a variety of biosensing and biomedical applications. In particular, self-assembled nanostructures of small organic molecules and peptides with intriguing characteristics (e.g., structure tailoring, facile processability, and excellent biocompatibility) have shown outstanding potential in the development of various biosensors. In this review, we introduced the unique properties of self-assembled nanostructures with small organic molecules and peptides for biosensing applications. We first discussed the applications of such nanostructures in electrochemical biosensors as electrode supports for enzymes and cells and as signal labels with a large number of electroactive units for signal amplification. Secondly, the utilization of fluorescent nanomaterials by self-assembled dyes or peptides was introduced. Thereinto, typical examples based on target-responsive aggregation-induced emission and decomposition-induced fluorescent enhancement were discussed. Finally, the applications of self-assembled nanomaterials in the colorimetric assays were summarized. We also briefly addressed the challenges and future prospects of biosensors based on self-assembled nanostructures.

Peptide- and Metabolite-Based Hydrogels: Minimalistic Approach for the Identification and Characterization of Gelating Building Blocks

Minimalistic peptide- and metabolite-based supramolecular hydrogels have great potential relative to traditional polymeric hydrogels in various biomedical and technological applications. Advantages such as remarkable biodegradability, high water content, favorable mechanical properties, biocompatibility, self-healing, synthetic feasibility, low cost, easy design, biological function, remarkable injectability, and multi-responsiveness to external stimuli make supramolecular hydrogels promising candidates for drug delivery, tissue engineering, tissue regeneration, and wound healing. Non-covalent interactions such as hydrogen bonding, hydrophobic interactions, electrostatic interactions, and π-π stacking interactions play key roles in the formation of peptide- and metabolite-containing low-molecular-weight hydrogels. Peptide- and metabolite-based hydrogels display shear-thinning and immediate recovery behavior due to the involvement of weak non-covalent interactions, making them supreme models for the delivery of drug molecules. In the areas of regenerative medicine, tissue engineering, pre-clinical evaluation, and numerous other biomedical applications, peptide- and metabolite-based hydrogelators with rationally designed architectures have intriguing uses. In this review, we summarize the recent advancements in the field of peptide- and metabolite-based hydrogels, including their modifications using a minimalistic building-blocks approach for various applications.

Unveiling the Role of Capping Groups in Naphthalene N-Capped Dehydrodipeptide Hydrogels

Self-assembled peptide-based hydrogels are archetypical nanostructured materials with a plethora of foreseeable applications in nanomedicine and as biomaterials. N-protected di- and tri-peptides are effective minimalist (molecular) hydrogelators. Independent variation of the capping group, peptide sequence and side chain modifications allows a wide chemical space to be explored and hydrogel properties to be tuned. In this work, we report the synthesis of a focused library of dehydrodipeptides N-protected with 1-naphthoyl and 2-naphthylacetyl groups. The 2-naphthylacetyl group was extensively reported for preparation of peptide-based self-assembled hydrogels, whereas the 1-naphthaloyl group was largely overlooked, owing presumably to the lack of a methylene linker between the naphthalene aromatic ring and the peptide backbone. Interestingly, dehydrodipeptides N-capped with the 1-naphthyl moiety afford stronger gels, at lower concentrations, than the 2-naphthylacetyl-capped dehydrodipeptides. Fluorescence and circular dichroism spectroscopy showed that the self-assembly of the dehydrodipeptides is driven by intermolecular aromatic π-π stacking interactions. Molecular dynamics simulations revealed that the 1-naphthoyl group allows higher order aromatic π-π stacking of the peptide molecules than the 2-naphthylacetyl group, together with hydrogen bonding of the peptide scaffold. The nanostructure of the gel networks was studied by TEM and STEM microscopy and was found to correlate well with the elasticity of the gels. This study contributes to understanding the interplay between peptide and capping group structure on the formation of self-assembled low-molecular-weight peptide hydrogels. Moreover, the results presented here add the 1-naphthoyl group to the palette of capping groups available for the preparation of efficacious low-molecular-weight peptide-based hydrogels.

Lipidation of Naturally Occurring α-Helical Antimicrobial Peptides as a Promising Strategy for Drug Design

In this paper, we describe the chemical synthesis, preliminary evaluation of antimicrobial properties and mechanisms of action of a novel group of lipidated derivatives of three naturally occurring α-helical antimicrobial peptides, LL-I (VNWKKVLGKIIKVAK-NH₂), LK6 (IKKILSKILLKKL-NH₂), ATRA-1 (KRFKKFFKKLK-NH₂). The obtained results showed that biological properties of the final compounds were defined both by the length of the fatty acid and by the structural and physico-chemical properties of the initial peptide. We consider C₈-C₁₂ length of the hydrocarbon chain as the optimal for antimicrobial activity improvement. However, the most active analogues exerted relatively high cytotoxicity toward keratinocytes, with the exception of the ATRA-1 derivatives, which had a higher selectivity for microbial cells. The ATRA-1 derivatives had relatively low cytotoxicity against healthy human keratinocytes but high cytotoxicity against human breast cancer cells. Taking into account that ATRA-1 analogues carry the highest positive net charge, it can be assumed that this feature contributes to cell selectivity. As expected, the studied lipopeptides showed a strong tendency to self-assembly into fibrils and/or elongated and spherical micelles, with the least cytotoxic ATRA-1 derivatives forming apparently smaller assemblies. The results of the study also confirmed that the bacterial cell membrane is the target for the studied compounds.

Accessing the Thiol Toolbox: Synthesis and Structure-Activity Studies on Fluoro-Thiol Conjugated Antimicrobial Peptides

The para-fluoro-thiol reaction (PFTR) is a modern name for the much older concept of a nucleophilic aromatic substitution reaction in which the para-position fluorine of a perfluorinated benzene moiety is substituted by a thiol. As a rapid and mild reaction, the PFTR is a useful technique for the post-synthetic modification of macromolecules like peptides on the solid phase. This reaction is of great potential since it allows for peptide chemists to access the vast catalogue of commercially available thiols with diverse structures to conjugate to peptides, which may impart favorable biological activity, particularly in antimicrobial sequences. This work covers the generation of a library of antimicrobial peptides by modifying a relatively inactive tetrapeptide with thiols of various structures using the PFTR to grant antimicrobial potency to the core sequence. In general, nucleophilic substitution of the peptide scaffold by hydrophobic thiols like cyclohexanethiol and octanethiol imparted the greatest antimicrobial activity over that of hydrophilic thiols bearing carboxylic acid or sugar moieties, which were ineffectual at improving the antimicrobial activity. The general trend here follows expected structure-activity relationship outcomes like that of changing the acyl group of lipopeptide antibiotics and is encouraging for the use of this reaction for structural modifications of antimicrobial sequences further.

Peptide Inhibitors of Insulin Fibrillation: Current and Future Challenges

Amyloidoses include a large variety of local and systemic diseases that share the common feature of protein unfolding or refolding into amyloid fibrils. The most studied amyloids are those directly involved in neurodegenerative diseases, while others, such as those formed by insulin, are surprisingly far less studied. Insulin is a very important polypeptide that plays a variety of biological roles and, first and foremost, is at the basis of the therapy of diabetic patients. It is well-known that it can form fibrils at the site of injection, leading to inflammation and immune response, in addition to other side effects. In this concise review, we analyze the current knowledge on insulin fibrillation, with a focus on the development of peptide-based inhibitors, which are promising candidates for their biocompatibility but still pose challenges to their effective use in therapy.

Antibacterial and Antibiofilm Properties of Self-Assembled Dipeptide Nanotubes

Over recent decades, multidrug-resistant pathogens have become a global concern, with WHO even considering it one of the biggest threats to global health, food security, and development today, which led to the search for alternative antibacterial agents. A special class is formed by peptides composed by the diphenylalanine motif whose antibacterial properties result from their supramolecular arrangement into nanotubes. However, several other dipeptides that also form nanotubes have been largely overlooked. Here, we present the antibacterial activity of four dipeptide nanotubes. The results point to diverse mechanisms through which dipeptide nanotubes exert their effect against bacteria. Antibacterial activity was similar for dipeptide nanotubes sufficiently wide to allow water flux while dipeptides displaying smaller channels were inactive. This suggests that two of the tested dipeptides, L-Phe-L-Phe (FF, diphenylalanine) and L-Leu-L-Ser (LS), are pore forming structures able to induce membrane permeation and affect cellular hydration and integrity. Of these two dipeptides, only FF demonstrated potential to inhibit biofilm formation. The amyloid-like nature and hydrophobicity of diphenylalanine assemblies are probably responsible for their adhesion to cell surfaces preventing biofilm formation and bacteria attachment.

Importance of Solvent-Bridged Structures of Fluorinated Diphenylalanines: Synthesis, Detailed NMR Analysis, and Rotational Profiles of Phe(2-F)-Phe(2-F), Phe(2-F)-Phe, and Phe-Phe(2-F)

The crystal structure of l-phenylalanyl l-phenylalanine (Phe-Phe, FF, a.k.a. diphenylalanine) is not merely noncentrosymmetric, but it is highly dipole parallel aligned. It is for this reason that FF is a nonlinear optical (NLO) material and exhibits strong second harmonic generation (SHG). Enhancement of the SHG response by ortho fluorination was demonstrated. Crystallization is nontrivial, and learning about the zwitterion structures in solution is important for the rational improvement of the crystallization process. Here, we present an NMR study of di-fluorinated FF (Phe(2-F)-Phe(2-F)) and mono-fluorinated FF isomers (Phe(2-F)-Phe and Phe-Phe(2-F)). The dipeptides were prepared by solid-phase synthesis and purified by high-performance liquid chromatography (HPLC). Their ¹H and ¹³C NMR spectra were recorded in partially deuterated water (10% D₂O), and two-dimensional (2D) NMR techniques were employed for signal assignments. The unambiguous assignments are reported of all chemical shifts for the aliphatic H and C atoms and of the C atoms of the carboxylate, the amide carbonyl, the CF carbons, and of every arene C atom in each phenyl ring. The dipeptides are trans amides and intramolecular hydrogen bonding between the ammonium group and the amide carbonyl restricts the H₃N-CH-C(O) geometry. We explored the rotational profile of the diphenylalanines as a function of the τ = ∠(C-N-C-CO₂) dihedral angle at the SMD(B3LYP/6-31G*) level without and with specific hydration and report the associated Karplus curves J(θ) vs θ = ∠(H-N-C-H). The rotational profiles show a maximum of three stationary structures, and relative conformer stabilities of the free diphenylalanines show that the conformation found in the crystal M1 is the least stable among the three, M3 > M2 ≫ M1. Specific water solvation makes all of the difference and adds a large competitive advantage to the water-bridged ion pair M1a. In fact, M1a becomes the most stable and dominant conformation for the parent diphenylalanine and mono1 F-FF and M1a becomes competitive with M3c for mono2 F-FF and di F-FF. Implications are discussed regarding the importance of the conformational preorganization of diphenylalanines in solution and the facility for their crystallization.

Hydrogelation tunability of bioinspired short peptides

Supramolecular assemblies of short peptides are experiencing a stimulating flowering. Herein, we report a novel class of bioinspired pentapeptides, not bearing Phe, that form hydrogels with fibrillar structures. The inherent sequence comes from the fragment 269-273 of nucleophosmin 1 protein, that is normally involved in liquid-liquid phase separation processes into the nucleolus. By means of rheology, spectroscopy, and scanning microscopy the crucial roles of the extremities in the modulation of the mechanical properties of hydrogels were elucidated. Three of four peptide showed a typical shear-thinning profile and a self-assembly into hierarchical nanostructures fibers and two of them resulted biocompatible in MCF7 cells. The presence of an amide group at C-terminal extremity caused the fastest aggregation and the major content of structured intermediates during gelling process. The tunable mechanical and structural features of this class of hydrogels render derived supramolecular systems versatile and suitable for future biomedical applications.

Heterochiral dipeptide d-phenylalanyl- l-phenylalanine (H-D Phe-L Phe-OH) as a potential inducer of metastatic suppressor NM23H1 in p53 wild-type and mutant cells

In recent years, significant progress has been made to the use-case of small peptides because of their diversified edifice and hence their versatile application scope in cancer therapy. Here we identify the heterochiral dipeptide H-^D Phe-^L Phe-OH (F1) as a potent inducer of the metastatic suppressor NM23H1. We divulge the effect of F1 on the major EMT/metastasis-associated genes and the implications on the invasion and migration ability of cancer cells. The anti-invasive potential of F1 was directly correlated with NM23H1 expression. Mechanistically, F1 treatment elevated p53 levels as validated by localization and transcriptional studies. In the NM23H1 knockdown condition, F1 failed to induce any p53 expression/nuclear localization, indicating that the upregulation in p53 expression by F1 is NM23H1 dependent. We also demonstrate how the antimetastatic potential of F1 is primarily mediated through NM23H1 irrespective of the p53 status of the cell. However, both NM23H1 and a functional p53 protein in conjunction govern the apoptotic and cytostatic potential of F1. Coimmunoprecipitation studies unraveled the augmentation of the p53 and NM23H1 interaction in p53 wild-type cells. However, in p53 mutated cells, no such enrichment was evidenced. We employed mouse isogenic cell lines (4T-1 and 4T-1 p53) to determine the in vivo efficacy of F1 (spontaneous and experimental models). Decreased tumor volume in the cohort injected with 4T-1 p53 cells demonstrated that while the antimetastatic potential of F1 was reliant on NM23H1, p53 activation was required for ablation of primary tumor burden. Our findings unravel that F1 treatment induces significant abrogation of the migration, invasion and metastatic potential of both p53 wild-type and p53 deficient cancers mediated through NM23H1.

Probing the self-assembly and anti-glioblastoma efficacy of a cinnamoyl-capped dipeptide hydrogelator

Herein, we introduce the first diphenylalanine dipeptide hydrogelator capped with the cinnamoyl functional group (Cin-L-F-L-F). We evaluate the effects of the cinnamoyl moiety on molecular self-assembly events and resultant physical properties of the hydrogel formed. In addition, we report our preliminary results of this dipeptide's cytotoxicity against glioblastoma (GBM) cancer cells.

Short Peptide-Based Smart Thixotropic Hydrogels †

Thixotropy is a fascinating feature present in many gel systems that has garnered a lot of attention in the medical field in recent decades. When shear stress is applied, the gel transforms into sol and immediately returns to its original state when resting. The thixotropic nature of the hydrogel has inspired scientists to entrap and release enzymes, therapeutics, and other substances inside the human body, where the gel acts as a drug reservoir and can sustainably release therapeutics. Furthermore, thixotropic hydrogels have been widely used in various therapeutic applications, including drug delivery, cornea regeneration and osteogenesis, to name a few. Because of their inherent biocompatibility and structural diversity, peptides are at the forefront of cutting-edge research in this context. This review will discuss the rational design and self-assembly of peptide-based thixotropic hydrogels with some representative examples, followed by their biomedical applications.

Atomic insight into short helical peptide comprised of consecutive multiple aromatic residues

The occurrence of sequential multiple aromatic residues in a helical sequence is rare compared to the β-sheet rich structure. Here, using helix promoting α-aminoisobutyric acid (Aib) residues, we unravel atomistic details of the helical secondary structure formation and the super helical assembly of two heptapeptides composed of sequential five and six phenylalanine (Phe) residues.

Structural Properties of Phenylalanine-Based Dimers Revealed Using IR Action Spectroscopy

Peptide segments with phenylalanine residues are commonly found in proteins that are related to neurodegenerative diseases. However, the self-assembly of phenylalanine-based peptides can be also functional. Peptides containing phenylalanine residues with different side caps, composition, and chemical alteration can form different types of nanostructures that find many applications in technology and medicine. Various studies have been performed in order to explain the remarkable stability of the resulting nanostructures. Here, we study the early stages of self-assembly of two phenylalanine derived peptides in the gas phase using IR action spectroscopy. Our focus lies on the identification of the key intra- and intermolecular interactions that govern the formation of the dimers. The far-IR region allowed us to distinguish between structural families and to assign the 2-(2-amino-2-phenylacetamido)-2-phenylacetic acid (PhgPhg) dimer to a very symmetric structure with two intermolecular hydrogen bonds and its aromatic rings folded away from the backbone. By comparison with the phenylalanine-based peptide cyclic L-phenylalanyl-L-phenylalanine (cyclo-FF), we found that the linear FF dimer likely adopts a less ordered structure. However, when one more phenylalanine residue is added (FFF), a more structurally organized dimer is formed with several intermolecular hydrogen bonds.

Emerging low-molecular weight nucleopeptide-based hydrogels: state of the art, applications, challenges and perspectives

Over the last twenty years, low-molecular weight gelators and, in particular, peptide-based hydrogels, have drawn great attention from scientists thanks to both their inherent advantages in terms of properties and their high modularity (e.g., number and nature of the amino acids). These supramolecular hydrogels originate from specific peptide self-assembly processes that can be driven, modulated and optimized via specific chemical modifications brought to the peptide sequence. Among them, the incorporation of nucleobases, another class of biomolecules well-known for their abilities to self-assemble, has recently appeared as a new promising and burgeoning approach to finely design supramolecular hydrogels. In this minireview, we would like to highlight the interest, high potential, applications and perspectives of these innovative and emerging low-molecular weight nucleopeptide-based hydrogels.

Structures of synthetic helical filaments and tubes based on peptide and peptido-mimetic polymers

Synthetic peptide and peptido-mimetic filaments and tubes represent a diverse class of nanomaterials with a broad range of potential applications, such as drug delivery, vaccine development, synthetic catalyst design, encapsulation, and energy transduction. The structures of these filaments comprise supramolecular polymers based on helical arrangements of subunits that can be derived from self-assembly of monomers based on diverse structural motifs. In recent years, structural analyses of these materials at near-atomic resolution (NAR) have yielded critical insights into the relationship between sequence, local conformation, and higher-order structure and morphology. This structural information offers the opportunity for development of new tools to facilitate the predictable and reproduciblede novodesign of synthetic helical filaments. However, these studies have also revealed several significant impediments to the latter process – most notably, the common occurrence of structural polymorphism due to the lability of helical symmetry in structural space. This article summarizes the current state of knowledge on the structures of designed peptide and peptido-mimetic filamentous assemblies, with a focus on structures that have been solved to NAR for which reliable atomic models are available.

Backbone extension via peptidomimetics at N-terminal; self-assembled nanofibrous cluster and application to selective progesterone detection in an aqueous medium

Despite the adequacy of the endogenous steroid (progesterone) levels in biological functioning, elevated levels of progesterone hormone have several physiological effects that are amplified due to its direct and indirect uptake from the environment, food products, and medical therapy. So, it is much needed to evaluate the progesterone levels in environmental samples as well as for biological fluids. In this work, we focused on the development of the nano sensing probe for the selective detection of progesterone among the library of steroid hormones belonging to the class of female sex hormones. Herein, functionalization of dipeptide is carried out at N-terminal to produce N-functionalized dipeptide (SS3), and simultaneously, its self-assembly properties are explored. Furthermore, HR-TEM imaging was also performed to examine the morphology of the self-assembled architectures before and after the addition of the steroid hormone. To investigate the binding mechanism of the sensing probe, Fluorescence spectroscopy, Circular Dichroism (CD), MD-Simulation, and DFT studies were performed and studied in detail. Moreover, to check the potency of the real-time application of the developed nanoprobe, we have successfully determined the spiked concentration of progesterone levels in pharmaceutical and biological fluid samples with functional percentage recovery. Also, the stability and other competitive binding studies of the probe with the coexisting substances are performed to check the rationality of the sensing probe at physiological conditions.

Fluorine Effect in the Gelation Ability of Low Molecular Weight Gelators

The three gelators presented in this work (Boc-D-Phe-L-Oxd-OH F0, Boc-D-F₁Phe-L-Oxd-OH F1 and Boc-D-F₂Phe-L-Oxd-OH F2) share the same scaffold and differ in the number of fluorine atoms linked to the aromatic ring of phenylalanine. They have been applied to the preparation of gels in 0.5% or 1.0% w/v concentration, using three methodologies: solvent switch, pH change and calcium ions addition. The general trend is an increased tendency to form structured materials from F0 to F1 and F2. This property ends up in the formation of stronger materials when fluorine atoms are present. Some samples, generally formed by F1 or F2 in 0.5% w/v concentration, show high transparency but low mechanical properties. Two gels, both containing fluorine atoms, show increased stiffness coupled with high transparency. The biocompatibility of the gelators was assessed exposing them to fibroblast cells and demonstrated that F1 and F2 are not toxic to cells even in high concentration, while F0 is not toxic to cells only in a low concentration. In conclusion, the presence of even only one fluorine atom improves all the gelators properties: the gelation ability of the compound, the rheological properties and the transparency of the final materials and the gelator biocompatibility.

Bio inspired growth factor loaded self assembling peptide nano hydrogel for chronic wound healing

Self assembling peptidebased hydrogel has been explored for delivering growth factors, anticancer drugs, antibiotics etc. Here, RADA 16-I (RADARADARADARADA), an ionic self complementary peptide that forms a well defined nanohydrogel has been studied for its ability to deliver PDGF-BB in a sustained manner and to destruct biofilm formed by wound specific pathogens. Results of the structural analysis of the nanohydrogel studied through AFM, FeSEM, CD, FT-IR and Rheometry, revealed the hydrogel forming ability of RADA 16-I with stable β-sheet structure at room temperature. The nanohydrogel was also found to destruct the biofilm formed under in vitro condition using S. aureus, E. coli and P. aeruginosa. The growth factor incorporated in the nanohydrogel followed first order release kinetics and showed sustained release up to 48 h. Angiogenic potential and wound healing ability of PDGF-BB incorporated nanohydrogel was confirmed in both in vitro and in vivo conditions. The animals treated with PDGF-BB incorporated nanohydrogel exhibited 99.5% wound closure at day 21. The content of hydroxyproline and ascorbic acid was significantly high in the treated animals when compared to control and untreated animals. Overall, the study provides the essential information and data for using RADA 16-I for treating chronic wounds.

Peptide Self-Assembled Nanostructures: From Models to Therapeutic Peptides

Self-assembly is the most suitable approach to obtaining peptide-based materials on the nano- and mesoscopic scales. Applications span from peptide drugs for personalized therapy to light harvesting and electron conductive media for solar energy production and bioelectronics, respectively. In this study, we will discuss the self-assembly of selected model and bioactive peptides, in particular reviewing our recent work on the formation of peptide architectures of nano- and mesoscopic size in solution and on solid substrates. The hierarchical and cooperative characters of peptide self-assembly will be highlighted, focusing on the structural and dynamical properties of the peptide building blocks and on the nature of the intermolecular interactions driving the aggregation phenomena in a given environment. These results will pave the way for the understanding of the still-debated mechanism of action of an antimicrobial peptide (trichogin GA IV) and the pharmacokinetic properties of a peptide drug (semaglutide) currently in use for the therapy of type-II diabetes.

Self-assembly of Fmoc-amino acids in capillary confined space forming parallel ordered fiber network for application of vascularization

Matrix formed by self-assembly of amino acids and their derivatives are suitable for cell spreading, migration and proliferation, and widely used in tissue engineering and organ regeneration, due to the...

Diffusion-controlled release of the theranostic protein-photosensitizer Azulitox from composite of Fmoc-Phenylalanine Fibrils encapsulated with BSA hydrogels

Hydrogels offer a promising potential for the encapsulation and regulated release of drugs due to their biocompatibility and their tunable properties as materials. Only a limited number of systems and procedures enable the encapsulation of sensitive proteins. N-terminally fmoc-protected phenylalanine has been shown to self-assemble into a transparent, stable hydrogel It can be considered a supergelator due to the low amount of monomers necessary for hydrogelation (0.1% w/v), making it a good candidate for the encapsulation and stabilization of sensitive proteins. However, application options for this hydrogel are rather limited to those of many other fibril-based materials due to its intrinsic lack of mechanical strength and high susceptibility to changes in environmental conditions. Here, we demonstrate that the stability of a fibrillary system and the resulting release of the protein-photosensitizer Azulitox can be increased by combining the hydrogel with a tightly cross-linked BSA hydrogel. Azulitox is known to display cell-penetrating properties, anti-proliferative activity and has a distinctive fluorescence. Confocal microscopy and fluorescence measurements verified the maintenance of all essential functions of the encapsulated protein. In contrast, the combination of fibrillary and protein hydrogel resulted in a significant stabilization of the matrix and an adjustable release pattern for encapsulated protein.

Mechanism of Amyloid Gel Formation by Several Short Amyloidogenic Peptides

Under certain conditions, many proteins/peptides are capable of self-assembly into various supramolecular formations: fibrils, films, amyloid gels. Such formations can be associated with pathological phenomena, for example, with various neurodegenerative diseases in humans (Alzheimer’s, Parkinson’s and others), or perform various functions in the body, both in humans and in representatives of other domains of life. Recently, more and more data have appeared confirming the ability of many known and, probably, not yet studied proteins/peptides, to self-assemble into quaternary structures. Fibrils, biofilms and amyloid gels are promising objects for the developing field of research of nanobiotechnology. To develop methods for obtaining nanobiomaterials with desired properties, it is necessary to study the mechanism of such structure formation, as well as the influence of various factors on this process. In this work, we present the results of a study of the structure of biogels formed by four 10-membered amyloidogenic peptides: the VDSWNVLVAG peptide (AspNB) and its analogue VESWNVLVAG (GluNB), which are amyloidogenic fragments of the glucantransferase Bgl2p protein from a yeast cell wall, and amyloidogenic peptides Aβ(31–40), Aβ(33–42) from the Aβ(1–42) peptide. Based on the analysis of the data, we propose a possible mechanism for the formation of amyloid gels with these peptides.

Triggering a transient organo-gelation system in a chemically active solvent

A transient organo-gelation system with spatiotemporal dynamic properties is described. Here, the solvent actively controls a complex set of equilibria that underpin the dynamic assembly event. The observed metastability is due to the in situ formation of a secondary solvent, acting as an antagonist against the primary solvent of the organogel.

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.

Pepsin Digest of Gliadin Forms Spontaneously Amyloid-Like Nanostructures Influencing the Expression of Selected Pro-Inflammatory, Chemoattractant, and Apoptotic Genes in Caco-2 Cells: Implications for Gluten-Related Disorders

SCOPE

Proteolysis-resistant gliadin peptides are intensely investigated in biomedical research relates to celiac disease and gluten-related disorders. Herein, the first integrated supramolecular investigation of pepsin-digested gliadin peptides (p-gliadin) is presented in combination with its functional behavior in the Caco-2 cell line.

METHODS AND RESULTS

First, gliadins are degraded by pepsin at pH 3, and the physicochemical properties of p-gliadin are compared with gliadin. An integrated approach using interfacial, spectroscopic, and microscopic techniques reveals that the p-gliadin forms spontaneously soluble large supramolecular structures, mainly oligomers and fibrils, capable of binding amyloid-sensitive dyes. The self-assembly of p-gliadin starts at a concentration of 0.40 µg mL^-1 . Second, the stimulation of Caco-2 cells with the p-gliadin supramolecular system is performed, and the mRNA expression levels of a panel of genes are tested. The experiments show that p-gliadin composed of supramolecular structures triggers significant mRNA up-regulation (p < 0.05) of pro-apoptotic biomarkers (ratio Bcl2/Bak-1), chemokines (CCL2, CCL3, CCL4, CCL5, CXCL8), and the chemokine receptor CXCR3.

CONCLUSIONS

This work demonstrates that p-gliadin is interfacial active, forming spontaneously amyloid-type structures that trigger genes in the Caco-2 cell line involved in recruiting specialized immune cells.

Supramolecular Antiparallel β-Sheet Formation by Tetrapeptides Based on Amyloid Sequence

Self-assembly of short peptides has emerged as an interesting research field for a wide range of applications. Recently, several truncated fragments of long-chain peptides or proteins responsible for different neurodegenerative diseases were studied to understand whether they can mimic the property and function of native peptides or not. It was reported that such a kind of peptide adopts a β-sheet structure in the disease state. It was observed that aromatic amino acid-rich peptide fragments possess a high tendency to adopt a β-sheet conformation. In this article, we are first time reporting the crystal structure of two tetrapeptides: Boc-GAII-OMe (Peptide 1) and Boc-GGVV-OMe (Peptide 2), composed of aliphatic amino acids, and the sequences are similar to the Aβ-peptide fragments Aβ_29-32 and Aβ_37-40 , respectively. In the solid-state, they are self-assembled in an antiparallel β-sheet fashion. The peptide units are connected by the strong amide hydrogen-bonding (N-H···O) interactions. Apart from that, other noncovalent interactions are also present, which help to stabilize the cross-β-sheet arrangement. Interestingly, in the crystal structure of Peptide 1, noncovalent C···C interaction between the electron-deficient carbonyl carbon, and the electron-rich sp³-carbon atom is observed, which is quite rare in the literature. The calculated torsion angles for these peptides are lying in the β-sheet region of the Ramachandran plot. FT-IR studies also indicate the formation of an antiparallel β-sheet structure in the solid-state. Circular dichroism of the peptides in the aqueous solution also suggests the presence of predominantly β-sheet-like conformation in the aqueous solution. Under cross-polarized light, Congo Red stained both peptides showed green-gold color due to birefringence indicating their amyloidogenic nature. This result indicates that the short peptide composed of aliphatic amino acid is capable of forming a β-sheet structure in the absence of aromatic amino acid and also can mimic the function of the native amyloid peptide.

Peptide-Protein Interactions: From Drug Design to Supramolecular Biomaterials

The self-recognition and self-assembly of biomolecules are spontaneous processes that occur in Nature and allow the formation of ordered structures, at the nanoscale or even at the macroscale, under thermodynamic and kinetic equilibrium as a consequence of specific and local interactions. In particular, peptides and peptidomimetics play an elected role, as they may allow a rational approach to elucidate biological mechanisms to develop new drugs, biomaterials, catalysts, or semiconductors. The forces that rule self-recognition and self-assembly processes are weak interactions, such as hydrogen bonding, electrostatic attractions, and van der Waals forces, and they underlie the formation of the secondary structure (e.g., α-helix, β-sheet, polyproline II helix), which plays a key role in all biological processes. Here, we present recent and significant examples whereby design was successfully applied to attain the desired structural motifs toward function. These studies are important to understand the main interactions ruling the biological processes and the onset of many pathologies. The types of secondary structure adopted by peptides during self-assembly have a fundamental importance not only on the type of nano- or macro-structure formed but also on the properties of biomaterials, such as the types of interaction, encapsulation, non-covalent interaction, or covalent interaction, which are ultimately useful for applications in drug delivery.

Nanoscale Assembly of Functional Peptides with Divergent Programming Elements

Self-assembling peptides are being applied both in the biomedical area and as building blocks in nanotechnology. Their applications are closely linked to their modes of self-assembly, which determine the functional nanostructures that they form. This work brings together two structural elements that direct nanoscale self-association in divergent directions: proline as a β-breaker and the β-structure-associated diphenylalanine motif, into a single tripeptide sequence. Amino acid chirality was found to resolve the tension inherent to these conflicting self-assembly instructions. Stereoconfiguration determined the ability of each of the eight possible Pro-Phe-Phe stereoisomers to self-associate into diverse nanostructures, including nanoparticles, nanotapes, or fibrils, which yielded hydrogels with gel-to-sol transition at a physiologically relevant temperature. Three single-crystal structures and all-atom molecular dynamics simulations elucidated the ability of each peptide to establish key interactions to form long-range assemblies (i,e., stacks leading to gelling fibrils), medium-range assemblies (i.e., stacks yielding nanotapes), or short-range assemblies (i.e., dimers or trimers that further associated into nanoparticles). Importantly, diphenylalanine is known to serve as a binding site for pathological amyloids, potentially allowing these heterochiral systems to influence the fibrillization of other biologically relevant peptides. To probe this hypothesis, all eight Pro-Phe-Phe stereoisomers were tested in vitro on the Alzheimer's disease-associated Aβ(1-42) peptide. Indeed, one nonfibril-forming stereoisomer effectively inhibited Aβ fibrillization through multivalent binding between diphenylalanine motifs. This work thus defined heterochirality as a useful feature to strategically develop future therapeutics to interfere with pathological processes, with the additional value of resistance to protease-mediated degradation and biocompatibility.

Tuning the mechanistic pathways of peptide self-assembly by aromatic interactions

Herein, we have unravelled the key influence of aromatic interactions on the mechanistic pathways of peptide self-assembly by introducing suitable chromophores (pyrene vs. naphthalene). Although both self-assembled peptides are indistinguishable in their morphologies, this minor structural difference strongly affects the packing modes (parallel vs. antiparallel) and the corresponding self-assembly mechanism (cooperative vs. isodemsic).

Heterochiral tetrapeptide self-assembly into hydrogel biomaterials for hydrolase mimicry

Self-assembling short peptides have attracted great interest as enzyme mimics, especially if the catalytic activity resides solely in the supramolecular structure so that it can be switched on/off as needed by controlling assembly/disassembly. Among the various enzyme classes, hydrolases find wide application in biomaterials, and their mimetics often contain His residues, in addition to either divalent cations or other amino acids to mimic the catalytic site. This work reports two self-assembling tetrapeptides based on the Ser-His motif for catalysis and the Phe-Phe motif to drive amyloid structure formation. Both peptides form thermoreversible hydrogels in phosphate buffer at neutral pH that display a mild esterase-like activity, as demonstrated on the hydrolysis of 4-nitrophenyl acetate as a model substrate, although presence of Ser did not enhance catalytic activity. The systems are characterised by circular dichroism, transmission electron microscopy, oscillatory rheology and Thioflavin T fluorescence as an amyloid stain, to provide further insights that may assist the future design of improved supramolecular catalysts.