Kinetically trapped self-assembly in synthetic nucleopeptides and nucleotides

Nature uses thermodynamically unfavourable dynamic self-assembly to execute cellular functions frequently. A nucleopeptide and ATP formed a self-assembled hydrogel. The peptide and AMP were unable to form a hydrogel. Notably, when ATP was hydrolyzed to AMP in situ by an ATPase enzyme, the peptide-AMP composition remained a self-assembled hydrogel, showing unusual kinetically trapped self-assembly.

Synthesis of S- and N,S-Heterocycle-Dipeptide Conjugates for Supramolecular Hydrogel Formation

Small peptides with aromatic nuclei at the N-terminus have been shown to form bioactive, biocompatible, and biodegradable supramolecular peptide hydrogels. Novel heterocycle-dipeptide conjugates with potential biological activity or application as drug carriers were synthesized by using S-(benzo[b]thiophene) and N,S-(thieno [2,3-b]pyridine and thieno[2,3-b]quinoline) heterocycles as N-protective groups for dipeptides l-Phe-l-Phe and l-Phe-l-Leu. The synthesis involved coupling heterocyclic carboxylic acids with trifluoroacetate salts of ethyl l-phenylalanyl-l-phenylalaninate and ethyl l-phenylalanyl- l-leucinate using HBTU and Et3N, producing the corresponding six N-heterocycle-dipeptide ester conjugates, which were then hydrolyzed to the carboxylic acids. These conjugates were subjected to gelation tests in water starting from 0.4 wt% concentration of the conjugates, using a pH-lowering method with GdL. Among them, only the conjugate of benzo[b]thiophene with l-Phe-l-Phe-OH formed a hydrogel, with a gelation critical concentration of 0.15 wt% (GdL 0.6%) and a final pH of 6.8, which is important for biological applications. The hydrogel was characterized by STEM, revealing nanofibers with an average thickness of 17 nm that assemble into a 3D network capable of trapping water. Further rheological analysis demonstrated its viscoelastic behavior (G' = 3.03 × 103 Pa; G″ = 3.28 × 102 Pa), comparable to the extracellular matrix of certain human tissues, crucial for biomedical applications.

A Review on the Rheological Properties of Single Amino Acids and Short Dipeptide Gels

Self-assembled peptide-based hydrogels have attracted considerable interest from the research community. Particularly, low molecular weight gelators (LMWGs) consisting of amino acids and short peptides are highly suitable for biological applications owing to their facile synthesis and scalability, as well as their biocompatibility, biodegradability, and stability in physiological conditions. However, challenges in understanding the structure-property relationship and lack of design rules hinder the development of new gelators with the required properties for several applications. Hereby, in the plethora of peptide-based gelators, this review discusses the mechanical properties of single amino acid and dipeptide-based hydrogels. A mutual analysis of these systems allows us to highlight the relationship between the gel mechanical properties and amino acid sequence, preparation methods, or N capping groups. Additionally, recent advancements in the tuning of the gels' rheological properties are reviewed. In this way, the present review aims to help bridge the knowledge gap between structure and mechanical properties, easing the selection or design of peptides with the required properties for biological applications.

Assessment of the MARTINI 3 Performance for Short Peptide Self-Assembly

The coarse-grained MARTINI force field, initially developed for membranes, has proven to be an exceptional tool for investigating supramolecular peptide assemblies. Over the years, the force field underwent refinements to enhance accuracy, enabling, for example, the reproduction of protein-ligand interactions and constant pH behavior. However, these protein-focused improvements seem to have compromised its ability to model short peptide self-assembly. In this study, we assess the performance of MARTINI 3 in reproducing peptide self-assembly using the well-established diphenylalanine (FF) as our test case. Unlike its success in version 2.1, FF does not even exhibit aggregation in version 3. By systematically exploring parameters for the aromatic side chains and charged backbone beads, we established a parameter set that effectively reproduces tube formation. Remarkably, these parameter adjustments also replicate the self-assembly of other di- and tripeptides and coassemblies. Furthermore, our analysis uncovers pivotal insights for enhancing the performance of MARTINI in modeling short peptide self-assembly. Specifically, we identify issues stemming from overestimated hydrophilicity arising from charged termini and disruptions in π-stacking interactions due to insufficient planarity in aromatic groups and a discrepancy in intermolecular distances between this and backbone-backbone interactions. This investigation demonstrates that strategic modifications can harness the advancements offered by MARTINI 3 for the realm of short peptide self-assembly.

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.

Histidine-Containing Amphiphilic Peptide-Based Non-Cytotoxic Hydrogelator with Antibacterial Activity and Sustainable Drug Release

A histidine-based amphiphilic peptide (P) has been found to form an injectable transparent hydrogel in phosphate buffer solution over a pH range from 7.0 to 8.5 with an inherent antibacterial property. It also formed a hydrogel in water at pH = 6.7. The peptide self-assembles into a nanofibrillar network structure which is characterized by high-resolution transmission electron microscopy, field-emission scanning electron microscopy, atomic force microscopy, small-angle X-ray scattering, Fourier-transform infrared spectroscopy, and wide-angle powder X-ray diffraction. The hydrogel exhibits efficient antibacterial activity against both Gram-positive bacteria Staphylococcus aureus (S. aureus) and Gram-negative bacteria Escherichia coli (E. coli). The minimum inhibitory concentration of the hydrogel ranges from 20 to 100 μg/mL. The hydrogel is capable of encapsulation of the drugs naproxen (a non-steroidal anti-inflammatory drug), amoxicillin (an antibiotic), and doxorubicin, (an anticancer drug), but, selectively and sustainably, the gel releases naproxen, 84% being released in 84 h and amoxicillin was released more or less in same manner with that of the naproxen. The hydrogel is biocompatible with HEK 293T cells as well as NIH (mouse fibroblast cell line) cells and thus has potential as a potent antibacterial and drug releasing agent. Another remarkable feature of this hydrogel is its magnification property like a convex lens.

Beyond Sol-Gel: Molecular Gels with Different Transitions

The existence of sol–gel transitions is one of the most manifest properties of molecular gels. These transitions reflect their nature since they correspond to the association or dissociation of low weight molecules through non-covalent interactions to form the network constitutive of the gel. Most described molecular gels undergo only one gel-to-sol transition upon heating, and the reverse sol-to-gel transition upon cooling. It has been long observed that different conditions of formation could lead to gels with different morphologies, and that gels can undergo a transition from gel to crystals. However, more recent publications report molecular gels which exhibit additional transitions, for instance gel-to-gel transitions. This review surveys the molecular gels for which, in addition to sol–gel transitions, transitions of different nature have been reported: gel-to-gel transitions, gel-to-crystal transition, liquid–liquid phase separations, eutectic transformations, and synereses.

π-System Functionalization Transforms Amyloidogenic Peptide Fragment of Human Islet Amyloid Polypeptide into a Super Hydrogelator

While a considerable number of ultra-short/short amyloid peptides have been reported to form 3D supramolecular hydrogels, they all possess high minimum gelation concentration (MGC) (≥1 wt%), which preclude their applications. In this context, we demonstrate that functionalisation of a well-known amyloidogenic ultra-short peptide fragment NFGAIL (IAPf) of human Islet amyloid polypeptide with a π-system (Fluorenyl, Fm) at the N-terminus of the peptide (Fm-IAPf) yield not only highly thermostable hydrogel at physiological pH but also exhibited super gelator nature as the MGC (0.08 wt%) falls below 0.1 wt%. Various experimental results confirmed that aromatic π-π interactions from fluorenyl moieties and hydrogen bonding interactions between the IAPf drive the self-assembly/fibril formation. Fm-IAPf is the first super hydrogelator derived from amyloid-based ultra-short peptides, to the best of our knowledge. We strongly believe that this report, i. e., functionalization of an amyloid peptide with π-system, provides a lead to develop super hydrogelators from other amyloid-forming peptide fragments for their potential applications.

Molecular Engineering of Rigid Hydrogels Co-assembled from Collagenous Helical Peptides Based on a Single Triplet Motif

The potential of ultra-short peptides to self-assemble into well-ordered functional nanostructures makes them promising minimal components for mimicking the basic ingredient of nature and diverse biomaterials. However, selection and modular design of perfect de novo sequences are extremely tricky due to their vast possible combinatorial space. Moreover, a single amino acid substitution can drastically alter the supramolecular packing structure of short peptide assemblies. Here, we report the design of rigid hybrid hydrogels produced by sequence engineering of a new series of ultra-short collagen-mimicking tripeptides. Connecting glycine with different combinations of proline and its post-translational product 4-hydroxyproline, the single triplet motif, displays the natural collagen-helix-like structure. Improved mechanical rigidity is obtained via co-assembly with the non-collagenous hydrogelator, fluorenylmethoxycarbonyl (Fmoc) diphenylalanine. Characterizations of the supramolecular interactions that promote the self-supporting and self-healing properties of the co-assemblies are performed by physicochemical experiments and atomistic models. Our results clearly demonstrate the significance of sequence engineering to design functional peptide motifs with desired physicochemical and electromechanical properties and reveal co-assembly as a promising strategy for the utilization of small, readily accessible biomimetic building blocks to generate hybrid biomolecular assemblies with structural heterogeneity and functionality of natural materials.

Systems chemistry of peptide-assemblies for biochemical transformations

During the billions of years of the evolutionary journey, primitive polymers, involved in proto metabolic pathways with low catalytic activity, played critical roles in the emergence of modern enzymes with remarkable substrate specificity. The precise positioning of amino acid residues and the complex orchestrated interplay in the binding pockets of evolved enzymes promote covalent and non-covalent interactions to foster a diverse set of complex catalytic transformations. Recent efforts to emulate the structural and functional information of extant enzymes by minimal peptide based assemblies have attempted to provide a holistic approach that could help in discerning the prebiotic origins of catalytically active binding pockets of advanced proteins. In addition to the impressive sets of advanced biochemical transformations, catalytic promiscuity and cascade catalysis by such small molecule based dynamic systems can foreshadow the ancestral catalytic processes required for the onset of protometabolism. Looking beyond minimal systems that work close to equilibrium, catalytic systems and compartments under non-equilibrium conditions utilizing simple prebiotically relevant precursors have attempted to shed light on how bioenergetics played an essential role in chemical emergence of complex behaviour. Herein, we map out these recent works and progress where diverse sets of complex enzymatic transformations were demonstrated by utilizing minimal peptide based self-assembled systems. Further, we have attempted to cover the examples of peptide assemblies that could feature promiscuous activity and promote complex multistep cascade reaction networks. The review also covers a few recent examples of minimal transient catalytic assemblies under non-equilibrium conditions. This review attempts to provide a broad perspective for potentially programming functionality via rational selection of amino acid sequences leading towards minimal catalytic systems that resemble the traits of contemporary enzymes.

Single-atom substitution enables supramolecular diversity from dipeptide building blocks

Dipeptides are popular building blocks for supramolecular gels that do not persist in the environment and may find various applications. In this work, we show that a simple substitution on the aromatic side-chain of phenylalanine with either fluorine or iodine enables supramolecular diversity upon self-assembly at neutral pH, leading to hydrogels or crystals. Each building block is characterized by ¹H- and ¹³C-NMR spectroscopy, LC-MS, circular dichroism, and molecular models. The supramolecular behaviour is monitored with a variety of techniques, including circular dichroism, oscillatory rheology, transmission electron microscopy, attenuated total reflectance Fourier-transformed infrared spectroscopy, visible Raman spectroscopy, synchrotron-radiation single-crystal X-ray diffraction and UV Resonance Raman spectroscopy, allowing key differences to be pinpointed amongst the halogenated analogues.

Controlling Syneresis of Hydrogels Using Organic Salts

Supramolecular hydrogels can spontaneously undergo syneresis through fibre-fibre interactions and expel significant amounts of water upon aging. In this process, the hydrophobicity of fibres which regulates the 3D-rearrangement of the self-assembled structures during syneresis is important. Here, we show that we can control the hydrophobic microenvironment of gels by incorporating organic salts into the co-assembled gel fibres thereby enabling control of the macroscopic gel volume phase transition.

Self-Assembly of Unprotected Dipeptides into Hydrogels: Water-Channels Make the Difference

Unprotected dipeptides are attractive building blocks for environmentally friendly hydrogel biomaterials by virtue of their low‐cost and ease of preparation. This work investigates the self‐assembling behaviour of the distinct stereoisomers of Ile‐Phe and Phe‐Ile in phosphate buffered saline (PBS) to form hydrogels, using transmission electron microscopy (TEM), attenuated total reflectance infrared spectroscopy (ATR‐IR), circular dichroism (CD), and oscillatory rheometry. Each peptide purity and identity was also confirmed by ¹H‐ and ¹³C‐NMR spectroscopy and HPLC‐MS. Finally, single‐crystal XRD data allowed the key interactions responsible for the supramolecular packing into amphipathic layers or water‐channels to be revealed. The presence of the latter in the crystal structure is a distinctive feature of the only gelator of this work that self‐organizes into stable hydrogels, with fast kinetics and the highest elastic modulus amongst its structural isomers and stereoisomers.

Peptide-Based Supramolecular Systems Chemistry

Peptide-based supramolecular systems chemistry seeks to mimic the ability of life forms to use conserved sets of building blocks and chemical reactions to achieve a bewildering array of functions. Building on the design principles for short peptide-based nanomaterials with properties, such as self-assembly, recognition, catalysis, and actuation, are increasingly available. Peptide-based supramolecular systems chemistry is starting to address the far greater challenge of systems-level design to access complex functions that emerge when multiple reactions and interactions are coordinated and integrated. We discuss key features relevant to systems-level design, including regulating supramolecular order and disorder, development of active and adaptive systems by considering kinetic and thermodynamic design aspects and combinatorial dynamic covalent and noncovalent interactions. Finally, we discuss how structural and dynamic design concepts, including preorganization and induced fit, are critical to the ability to develop adaptive materials with adaptive and tunable photonic, electronic, and catalytic properties. Finally, we highlight examples where multiple features are combined, resulting in chemical systems and materials that display adaptive properties that cannot be achieved without this level of integration.

Self-Assembly Dipeptide Hydrogel: The Structures and Properties

Self-assembly peptide-based hydrogels are well known and popular in biomedical applications due to the fact that they are readily controllable and have biocompatibility properties. A dipeptide is the shortest self-assembling motif of peptides. Due to its small size and simple synthesis method, dipeptide can provide a simple and easy-to-use method to study the mechanism of peptides' self-assembly. This review describes the design and structures of self-assembly linear dipeptide hydrogels. The strategies for preparing the new generation of linear dipeptide hydrogels can be divided into three categories based on the modification site of dipeptide: 1) COOH-terminal and N-terminal modified dipeptide, 2) C-terminal modified dipeptide, and 3) uncapped dipeptide. With a deeper understanding of the relationship between the structures and properties of dipeptides, we believe that dipeptide hydrogels have great potential application in preparing minimal biocompatible materials.

Tuneable Hybrid Hydrogels via Complementary Self-Assembly of a Bioactive Peptide with a Robust Polysaccharide

Synthetic materials designed for improved biomimicry of the extracellular matrix must contain fibrous, bioactive, and mechanical cues. Self-assembly of low molecular weight gelator (LMWG) peptides Fmoc-DIKVAV (Fmoc-aspartic acid-isoleucine-lysine-valine-alanine-valine) and Fmoc-FRGDF (Fmoc-phenylalanine-arginine-glycine-aspartic acid-phenylalanine) creates fibrous and bioactive hydrogels. Polysaccharides such as agarose are biocompatible, degradable, and non-toxic. Agarose and these Fmoc-peptides have both demonstrated efficacy in vitro and in vivo. These materials have complementary properties; agarose has known mechanics in the physiological range but is inert and would benefit from bioactive and topographical cues found in the fibrous, protein-rich extracellular matrix. Fmoc-DIKVAV and Fmoc-FRGDF are synthetic self-assembling peptides that present bioactive cues "IKVAV" and "RGD" designed from the ECM proteins laminin and fibronectin. The work presented here demonstrates that the addition of agarose to Fmoc-DIKVAV and Fmoc-FRGDF results in physical characteristics that are dependent on agarose concentration. The networks are peptide-dominated at low agarose concentrations, and agarose-dominated at high agarose concentrations, resulting in distinct changes in structural morphology. Interestingly, at mid-range agarose concentration, a hybrid network is formed with structural similarities to both peptide and agarose systems, demonstrating reinforced mechanical properties. Bioactive-LMWG polysaccharide hydrogels demonstrate controllable microenvironmental properties, providing the ability for tissue-specific biomaterial design for tissue engineering and 3D cell culture.

Controlling Nucleopeptide Hydrogel Self-Assembly and Formation for Cell-Culture Scaffold Applications

Hydrogels made from self-assembling peptides have significant advantages in tissue engineering, namely a biocompatible nature and large molecular repertoire. Short peptides in particular allow for straightforward synthesis, self-assembly, and reproducibility. Applications are currently limited, however, due to potential toxicity of the chemical modifications that drive self-assembly and harsh gelation conditions. Peptides conjugated to nucleobases present one opportunity for a naturally derived species to minimize cytotoxicity. We have developed a hydrogel-formation environment for nucleopeptide gelation modulated entirely by biological buffers and salts. Self-assembly in this system is dependent on buffer and ion identity mediated by pK_a and formulation in the former and by valency and ionicity in the latter. Solutions at physiological pH and osmolarity, and in turn compatible with cell culture, initiate hydrogel formation and analytical and computational methods are used to explore pH and salt effects at the molecular and structural level. The mechanism of nucleopeptide self-assembly enables tuning of mechanical properties through the addition of divalent cations and one order of magnitude increase in hydrogel storage modulus. The stability of these constructs therefore provides an opportunity for long-term cell culture, and we demonstrate survival and proliferation of fibroblasts on hydrogel surfaces. This novel, biological buffer-mediated gelation methodology expands opportunities for tissue engineering applications of short peptides and their derivatives.

Assembly of cationic and amphiphilic β-sheet FKF tripeptide confers antibacterial activity

The race drawn against bacteria facing the evolution of antimicrobial resistance fuels research for new drugs and therapeutic strategies. FKF, a tripeptide that is cationic and amphiphilic was examined in light of its potential antimicrobial activity. Acid titration of purified peptide solution, 6% w/v (136 mM), yielded a hydrogel at pH~ 4. Cryo-TEM images of FKF revealed distinct phases formed upon increase in pH, ranging from elongated needles, uniform width fibers, sheets and tubular structures. ¹H NMR attested FKF charged states as function of pH, and CD and FTIR measurements indicated that FKF β-sheet assemblies are held by both π-π stacking and H-bonds. FKF hydrogel displayed bactericidal activity against E. coli and P. aeruginosa with a 3-log reduction in bacterial counts. The hydrogel was also found effective in reducing P. aeruginosa contamination in a skin lesion model in rats. FKF forms a unique antimicrobial peptide-hydrogel, showing neglectable effect in dissolved state, yet only when fibrillary assembled it gains functionality. STATEMENT OF SIGNIFICANCE: Ultra-short peptides are at the frontier of peptide self-assembly research. The tripeptide FKF assumes distinct assembly forms that are a function of pH, for which we have pinpointed the accompanying changes in charge. Made of natural amino acids, FKF forms a pure peptide hydrogel phase, which is intrinsically antimicrobial. We demonstrate that antimicrobial effect is only assumed by the peptide assemblies, posing self-assembly as a pre-requisite for FKF's bactericidal effect. This system provides evidence for the link between specific microscopic peptide assembled structures, macroscopic gel formation and antimicrobial effect, utilized to alleviate bacterial contamination in vivo.

Peptide Gelators to Template Inorganic Nanoparticle Formation

The use of peptides to template inorganic nanoparticle formation has attracted great interest as a green route to advance structures with innovative physicochemical properties for a variety of applications that range from biomedicine and sensing, to catalysis. In particular, short-peptide gelators offer the advantage of providing dynamic supramolecular environments for the templating effect on the formation of inorganic nanoparticles directly in the resulting gels, and ideally without using further reductants or chemical reagents. This mini-review describes the recent progress in the field to outline future research directions towards dynamic functional materials that exploit the synergy between supramolecular chemistry, nanoscience, and the interface between organic and inorganic components for advanced performance.

Control of peptide hydrogel formation and stability via heating treatment

Heating treatment is widely used in the preparation of metallic materials with controlled phase behavior and mechanical properties. However, for the soft materials assembled by short peptides, especially simple dipeptides, the detailed influences of heating treatment on the structures and functions of the materials remain largely unexplored. Here we showed that by thermal annealing or quenching of aromatic peptide solutions under kinetic control, we are able to control the self-assembly of peptide into materials with distinct phase behavior and macroscopic properties. The thermal annealing of the heated peptide solutions will lead to the formation of large nanobelts or bundles in solution, and no gels will be formed. However, by quenching the heated peptide solution, a self-supporting hydrogel will be formed quickly. Structure analysis revealed that the peptides preferred to self-assembled into much thinner and flexible nanohelices during quenching treatment. Moreover, the stability of the gels further increased with the repeated heating and quenching cycling of the peptide solutions. The results demonstrated that the heat treatment can be used to control the structure and function of self-assembled materials in a way similar to that of the conventional metallic or alloy materials.

Self-Assembling, Ultrashort Peptide Gels as Antimicrobial Biomaterials

Supramolecular antimicrobial hydrogels based on peptides are attractive soft materials for the treatment of infections, considering their ease of preparation and benign fate in biological settings and in the environment. In particular, stimuli-responsive systems that can be assembled/disassembled ad hoc could offer the opportunity to switch on/off their bioactivity as needed. Besides, the shorter is the peptide, the lower its cost of production. However, a structure-to-function relationship is yet to be defined and reported activities are generally not yet competitive relative to traditional antibiotics. Inspiration for their design can be found in host defense peptides (HDPs), which can self-assemble to exert their function. This article reviews research developments in this emerging area, and it examines features, differences and similarities between antimicrobial and amyloid peptides to open the avenue towards the next generation of supramolecular antimicrobial peptides as innovative therapeutic materials.

Stimuli-Sensitive Self-Assembled Tubules Based on Lysine-Derived Surfactants for Delivery of Antimicrobial Proteins

Drug delivery vectors based on amphiphiles have important features such as versatile physicochemical properties and stimuli-responsiveness. Amino acid-based surfactants are especially promising amphiphiles due to their enhanced biocompatibility compared to conventional surfactants. They can self-organize into micelles, vesicles and complex hierarchical structures, such as fibers, twisted and coiled ribbons, and tubules. In this work, we investigated the self-assembly and drug loading properties of a family of novel anionic double-tailed lysine-derived surfactants, with variable degree of tail length mismatch, designated as mLys10 and 10Lysn, where m and n are the number of carbon atoms in the tails. These surfactants form tubular aggregates with assorted morphologies in water that undergo gelation due to dense entanglement, as evidenced by light and electron microscopy. Lysozyme (LZM), an enzyme with antimicrobial properties, was selected as model protein for loading. After the characterization of the interfacial properties and phase behavior of the amphiphiles, the LZM-loading ability of the tubules was investigated, under varying experimental conditions, to assess the efficiency of the aggregates as pH- and temperature-sensitive nanocarriers. Further, the toxicological profile of the surfactants per se and surfactant/LZM hydrogels was obtained, using human skin fibroblasts (BJ-5ta cell line). Overall, the results show that the tubule-based hydrogels exhibit very interesting properties for the transport and controlled release of molecules of therapeutic interest.

Selective release of a potent anticancer agent from a supramolecular hydrogel using green light

Selective green-light triggered release of an anticancer agent under physiological conditions from a supramolecular hydrogel.

Heterochirality and Halogenation Control Phe-Phe Hierarchical Assembly

Diphenylalanine is an amyloidogenic building block that can form a versatile array of supramolecular materials. Its shortcomings, however, include the uncontrolled hierarchical assembly into microtubes of heterogeneous size distribution and well-known cytotoxicity. This study rationalized heterochirality as a successful strategy to address both of these pitfalls and it provided an unprotected heterochiral dipeptide that self-organized into a homogeneous and optically clear hydrogel with excellent ability to sustain fibroblast cell proliferation and viability. Substitution of one l-amino acid with its d-enantiomer preserved the ability of the dipeptide to self-organize into nanotubes, as shown by single-crystal XRD analysis, whereby the pattern of electrostatic and hydrogen bonding interactions of the backbone was unaltered. The effect of heterochirality was manifested in subtle changes in the positioning of the aromatic side chains, which resulted in weaker intermolecular interactions between nanotubes. As a result, d-Phe-l-Phe self-organized into homogeneous nanofibrils with a diameter of 4 nm, corresponding to two layers of peptides around a water channel, and yielded a transparent hydrogel. In contrast with homochiral Phe-Phe stereoisomer, it formed stable hydrogels thermoreversibly. d-Phe-l-Phe displayed no amyloid toxicity in cell cultures with fibroblast cells proliferating in high numbers and viability on this biomaterial, marking it as a preferred substrate over tissue-culture plastic. Halogenation also enabled the tailoring of d-Phe-l-Phe self-organization. Fluorination allowed analogous supramolecular packing as confirmed by XRD, thus nanotube formation, and gave intermediate levels of bundling. In contrast, iodination was the most effective strategy to augment the stability of the resulting hydrogel, although at the expense of optical transparency and biocompatibility. Interestingly, iodine presence hindered the supramolecular packing into nanotubes, resulting instead into amphipathic layers of stacked peptides without the occurrence of halogen bonding. By unravelling fine details to control these materials at the meso- and macro-scale, this study significantly advanced our understanding of these systems.

Supramolecular hydrogels from unprotected dipeptides: a comparative study on stereoisomers and structural isomers

Amino acid stereoconfiguration has been shown to play a key role in the self-assembly of unprotected tripeptides into hydrogels under physiological conditions. Dramatic changes were noted for hydrophobic sequences based on the diphenylalanine motif from the formation of amorphous aggregates in the case of homochiral peptides to nanostructured and stable hydrogels in the case of heterochiral stereoisomers. Herein, we report that by further shortening the sequence to a dipeptide, the overall differences between isomers are less marked, with both homo- and hetero-chiral dipeptides forming gels, although with different stability over time. The soft materials are studied by a number of spectroscopic and microcopic techniques, and single-crystal X-ray diffraction to unveil the supramolecular interactions of these hydrogel building blocks.

Designing peptide nanoparticles for efficient brain delivery

The targeted delivery of therapeutic compounds to the brain is arguably the most significant open problem in drug delivery today. Nanoparticles (NPs) based on peptides and designed using the emerging principles of molecular engineering show enormous promise in overcoming many of the barriers to brain delivery faced by NPs made of more traditional materials. However, shortcomings in our understanding of peptide self-assembly and blood-brain barrier (BBB) transport mechanisms pose significant obstacles to progress in this area. In this review, we discuss recent work in engineering peptide nanocarriers for the delivery of therapeutic compounds to the brain: from synthesis, to self-assembly, to in vivo studies, as well as discussing in detail the biological hurdles that a nanoparticle must overcome to reach the brain.

Programming properties of transient hydrogels by an enzymatic reaction

Supramolecular gels are usually stable in time as they are formed under thermodynamic equilibrium or at least in a deep well of a kinetically trapped state. However, artificial construction of kinetically controlled transient supramolecular gels is an interesting challenge. In these systems, usually a kinetically trapped transient aggregate is formed by active building blocks that leads to gelation; the gel then typically returns to the solution state. In this work, we show that such transient aggregation can occur by successive formation of two distinctly different kinetically controlled metastable states. Control over the first metastable state allows us to achieve significant control over the stability and properties of the second metastable state.

Bioadhesive supramolecular hydrogel from unprotected, short d,l-peptides with Phe-Phe and Leu-Asp-Val motifs

The uncapped tripeptide DPhe-Phe-Leu acts as self-assembly template to yield supramolecular hydrogel biomaterials. As an example, self-assembling DPhe-Phe-Leu-Asp-Val contains the LDV bioadhesive motif for β1 integrin activation. Hydrogels made of the two peptides successfully mimic fibronectin of the extracellular matrix and lead to high cell viability, adhesion, and spreading.

Light-triggered syneresis of a water insoluble peptide-hydrogel effectively removes small molecule waste contaminants

A short peptide based hydrogel exhibits aqueous insolubility, thixotropy and efficient light induced syneresis. Upon irradiation with UV light, the hydrogel shrinks and expells ∼50% of the solvent. Syneresis is caused by light-triggered trans-cis isomerisation of an azobenzene moiety in the peptide derivative. This expulsion of solvent can be effectively exploited in the removal of low molecular weight contaminants in water.

Light-controlled self-assembly of a dithienylethene bolaamphiphile in water

In this work, we report the light-driven self-assembly of photochromic dithienylethene bolaamphiphiles in aqueous media. The open → closed transition that occurred upon irradiation was accompanied by the formation of 1D nanofibers.

A Comprehensive Study on Self-Assembly and Gelation of C13-Dipeptides-From Design Strategies to Functionalities

Computational and experimental methods were applied to investigate the self-assembly and gelation of C₁₃-dipeptides. A modified aggregation propensity (AP_S) was introduced to correlate the effects of side chains of amino acids on the tendency to aggregate. From the experimental results, the ranges of 0.156 < AP_S < 0.250 seemed to be a proper region for the C₁₃-dipeptides to form hydrogels, while other molecules with higher or lower AP_S were insoluble or dissociated. As observed from molecular dynamics simulations, the C₁₃-dipeptides first formed small aggregates through hydrophobic interactions and then rearranged through electrostatic attractions and hydrogen bonds for self-assembly. The C₁₃-dipeptides tended to be antiparallel packed, as shown by hydrogen bonding analyses. Experimental observations and analyses on the structures of C₁₃-dipeptide hydrogels matched the computational conclusions very well. From the five selected gelators, i.e., C₁₃-GW, C₁₃-VY, and C₁₃-WT, strong π-π stacking was observed. For C₁₃-WS, strong hydrogen bonding was found, and in C₁₃-WY, both strong π-π interactions and hydrogen bonds were found. It takes around 90 min or longer for C₁₃-dipeptides to form hydrogels, and those formed by C₁₃-WY and C₁₃-WS had weak water holding capacities, which might be due to strong intermolecular hydrogen bonding. From rheological studies, the C₁₃-dipeptides formed strong chemical gels that were stabilized by strong interactions between the molecular aggregates. These gelators exhibit the potentials to be environmentally friendly substitutes for the common functionalized peptide gelators.

Phase Separation in Supramolecular Hydrogels Based on Peptide Self-Assembly from Enzyme-Coated Nanoparticles

Spatial localization of biocatalysts, such as enzymes, has recently proven to be an effective process to direct supramolecular self-assemblies in a spatiotemporal way. In this work, silica nanoparticles (NPs) functionalized covalently by alkaline phosphatase (NPs@AP) induce the localized growth of self-assembled peptide nanofibers from NPs by dephosphorylation of Fmoc-FFpY peptides (Fmoc: fluorenylmethyloxycarbonyl; F: phenylalanine; Y: tyrosine; p: phosphate group). The fibrillary nanoarchitecture around NPs@AP underpins a homogeneous hydrogel, which unexpectedly undergoes a macroscopic shape change over time. This macroscopic change is due to a phase separation leading to a dense phase (in NPs and nanofibers) in the center of the vial and surrounded by a dilute one, which still contains NPs and peptide self-assemblies. We thus hypothesize that the phase separation is not a syneresis process. Such a change is only observed when the enzymes are localized on the NPs. The dense phase contracts with time until reaching a constant volume after several days. For a given phosphorylated peptide concentration, the dense phase contracts faster when the NPs@AP concentration is increased. For a given NPs@AP concentration, it condenses faster when the peptide concentration increases. We hypothesize that the appearance of a dense phase is not only due to attractive interactions between NPs@AP but also to the strong interactions of self-assembled peptide nanofibers with the enzymes, covalently fixed on the NPs.

A Self-Healing, All-Organic, Conducting, Composite Peptide Hydrogel as Pressure Sensor and Electrogenic Cell Soft Substrate

Conducting polymer hydrogels (CPHs) emerge as excellent functional materials, as they harness the advantages of conducting polymers with the mechanical properties and continuous 3D nanostructures of hydrogels. This bicomponent organization results in soft, all-organic, conducting micro-/nanostructures with multifarious material applications. However, the application of CPHs as functional materials for biomedical applications is currently limited due to the necessity to combine the features of biocompatibility, self-healing, and fine-tuning of the mechanical properties. To overcome this issue, we choose to combine a protected dipeptide as the supramolecular gelator, owing to its intrinsic biocompatibility and excellent gelation ability, with the conductive polymer polyaniline (PAni), which was polymerized in situ. Thus, a two-component, all-organic, conducting hydrogel was formed. Spectroscopic evidence reveals the formation of the emeraldine salt form of PAni by intrinsic doping. The composite hydrogel is mechanically rigid with a very high storage modulus ( G') value of ∼2 MPa, and the rigidity was tuned by changing the peptide concentration. The hydrogel exhibits ohmic conductivity, pressure sensitivity, and, importantly, self-healing features. By virtue of its self-healing property, the polymeric nonmetallic hydrogel can reinstate its intrinsic conductivity when two of its macroscopically separated blocks are rejoined. High cell viability of cardiomyocytes grown on the composite hydrogel demonstrates its noncytotoxicity. These combined attributes of the hydrogel allowed its utilization for dynamic range pressure sensing and as a conductive interface for electrogenic cardiac cells. The composite hydrogel supports cardiomyocyte organization into a spontaneously contracting system. The composite hydrogel thus has considerable potential for various applications.

Amyloid-Like Fibrillary Morphology Originated by Tyrosine-Containing Aromatic Hexapeptides

Phenylalanine-based nanostructures have attracted the attention of the material science community for their functional properties. These properties strongly depend on the hierarchic organization of the nanostructure that in turn can be finely tuned by punctual chemical modifications of the building blocks. Herein, we investigate how the partial or the complete replacement of the Phe residues in PEG₈ -(Phe)₆ (PEG₈ -F6) with tyrosines to generate PEG₈ -(Phe-Tyr)₃ (PEG₈ -(FY)3) or PEG₈ -(Tyr)₆ (PEG₈ -Y6) affects the structural/functional properties of the nanomaterial formed by the parental compound. Moreover, the effect of the PEG derivatization was evaluated through the characterization of the peptides without the PEG moiety (Tyr)₆ (Y6) and (Phe-Tyr)₃ ((FY)3). Both PEG₈ -Y6 and PEG₈ -(FY)3 can self-assemble in water at micromolar concentrations in β-sheet-rich nanostructures. However, WAXS diffraction patterns of these compounds present significant differences. PEG₈ -(FY)3 shows a 2D WAXS oriented fiber diffraction profile characterized by the concomitant presence of a 4.7 Å meridional and a 12.5 Å equatorial reflection that are generally associated with cross-β structure. On the other hand, the pattern of PEG₈ -Y6 is characterized by the presence of circles typically observed in the presence of PEG crystallization. Molecular modeling and dynamics provide an atomic structural model of the peptide spine of these compounds that is in good agreement with WAXS experimental data. Gelation phenomenon was only detected for PEG₈ -(FY)3 above a concentration of 1.0 wt % as confirmed by storage (G'≈100 Pa) and loss (G''≈28 Pa) moduli in rheological studies. The cell viability on CHO cells of this soft hydrogel was certified to be 90 % after 24 hours of incubation.

Structural Characterization of Self-Assembled Tetra-Tryptophan Based Nanostructures: Variations on a Common Theme

Over the years, a large number of multidisciplinary investigations has unveiled that the self-assembly of short peptides and even of individual amino acids can generate a variety of different biomaterials. In this framework, we have recently reported that polyethylene glycol (PEG) conjugates of short homopeptides, containing aromatic amino acids such as phenylalanine (Phe, F) and naphthylalanine (Nal), are able to form elongated fibrillary aggregates having interesting chemical and physical properties. We here extend these analyses characterizing the self-assembling propensity of PEG₆ -W4, a PEG adduct of the tetra-tryptophan (W4) sequence. A comprehensive structural characterization of PEG₆ -W4 was obtained, both in solution and at the solid state, through the combination of spectroscopic, microscopic, X-ray scattering and computational techniques. Collectively, these studies demonstrate that this peptide is able to self-assemble in fibrillary networks characterized by a cross β-structure spine. The present findings clearly demonstrate that aromatic residues display a general propensity to induce self-aggregation phenomenon, despite the significant differences in the physicochemical properties of their side chains.

Bicomponent β-sheet assembly of dipeptide fluorophores of opposite polarity and sensitive detection of nitro-explosives

Fluorescent hydrogels formed by the bicomponent β-sheet co-assembly of dipeptide–pyrene amphiphiles of opposite polarity provide a 3D microenvironment to detect toxic nitro-explosives.

Partially Acetylated or Benzoylated Arabinose Derivatives as Structurally Simple Organogelators: Effect of the Ester Protecting Group on Gel Properties

Sugar-based low-molecular-weight gelators (LMWGs) have been used for various applications for a long time. Herein, structurally simple, ester-protected arabinosides are reported as low-molecular-weight organogelators (LMOGs) that are able to gel aromatic solvents, as well as petrol and diesel. Studies on the mechanical strength of the gels, through detailed rheological experiments, indicate that gels from the 1,2-dibenzoylated arabinose gelator possess better mechanical properties than those from the 1,2-diacetylated gelator. These results are interpreted in terms of the tendency of the former to form fibers with comparatively lower diameter than those of the latter, based on detailed field-emission SEM and AFM studies. Investigations of the interactions responsible for the self-assembly of gelators through IR spectroscopy and wide-angle X-ray scattering reveal that the primary interactions responsible are hydrogen bonds between the hydroxyl groups and ester C=O, which is absent in the solid state of the gelators. In addition, π interactions present in the 1,2-dibenzoylated derivative result in a more regular arrangement, which, in turn, leads to better mechanical properties of the gels compared with those of the 1,2-diacetylated gelator.

Controlling the length of self-assembled nanotubes by sonication followed by polymer wrapping

In this work, we report that sonication, followed by polymer-wrapping, is an effective strategy to reduce the length of self-assembled nanotubes and suspend their propensity to self-heal into their elongated precursors.