Molecular Self-Assembly of Cyclic Dipeptide Derivatives and Their Applications

The high-throughput solid-phase extraction of cis-cyclo(L-Leu-L-Pro) and cis-cyclo(L-Phe-L-Pro) from Lactobacillus plantarum demonstrates efficacy against multidrug-resistant bacteria and influenza A (H3N2) virus

Introduction: 2,5-diketopiperazines are the simplest forms of cyclic dipeptides (CDPs) and have diverse frameworks with chiral side chains that are useful for drug development. Previous research has investigated the antimicrobial properties of proline-linked CDPs and their combinations in the culture filtrate (CF) of Lactobacillus plantarum LBP-K10 using anion exchange chromatography (AEC). However, the quantity of CDPs showcasing notable anti-influenza virus activity derived from AECs was generally lower than those originating from Lactobacillus CF. Methods: To address this issue, the study aims to propose a more efficient method for isolating CDPs and to introduce the antiviral combinations of CDPs obtained using a new method. The study employed a novel technique entailing high-throughput C18-based solid-phase extraction with a methanol gradient (MeSPE). The MeSPE method involved increasing the methanol concentration from 5% to 50% in 5% increments. Results: The methanol SPE fractions (MeSPEfs) eluted with methanol concentrations between 35% and 45% evinced substantial efficacy in inhibiting the influenza A/H3N2 virus via plaque-forming assay. MeSPEf-45, the 45% MeSPEf, exhibited exceptional efficacy in preventing viral infections in Madin-Darby kidney cells, surpassing both individual CDPs and the entire set of MeSPEfs. To identify the specific antiviral components of MeSPEf-45, all MeSPEfs were further fractionated through preparative high-performance liquid chromatography (prep-HPLC). MeSPEf-45 fractions S8 and S11 presented the highest activity against multidrug-resistant bacteria and influenza A/H3N2 virus among all MeSPEfs, with 11 common fractions. Antiviral fractions S8 and S11 were identified as proline-based CDPs, specifically cis-cyclo(L-Leu-L-Pro) and cis-cyclo(L-Phe-L-Pro), using gas chromatography-mass spectrometry. The combination of MeSPEf-45 fractions S8 and S11 displayed superior antibacterial and anti-influenza virus effects compared to the individual fractions S8 and S11. Discussion: High-throughput MeSPE-derived MeSPEfs and subsequent HPLC-fractionated fractions presents an innovative approach to selectively purify large amounts of potent antimicrobial CDPs from bacterial CF. The findings also show the effectiveness of physiologically bioactive combinations that utilize fractions not containing CDP. This study provides the initial evidence demonstrating the antimicrobial properties of CDPs acquired through high-throughput SPE techniques.

Hybrid molecules synergistically mitigate ferroptosis and amyloid-associated toxicities in Alzheimer's disease

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the build-up of extracellular amyloid β (Aβ) plaques and intracellular neurofibrillary tangles (NFTs). Ferroptosis, an iron (Fe)-dependent form of cell death plays a significant role in the multifaceted AD pathogenesis through generation of reactive oxygen species (ROS), mitochondrial damage, lipid peroxidation, and reduction in glutathione peroxidase 4 (GPX4) enzyme activity and levels. Aberrant liquid-liquid phase separation (LLPS) of tau drives the growth and maturation of NFTs contributing to AD pathogenesis. In this study, we strategically combined the structural and functional properties of gallic acid (GA) and cyclic dipeptides (CDPs) to synthesize hybrid molecules that effectively target both ferroptosis and amyloid toxicity in AD. This innovative approach marks a paradigm shift from conventional therapeutic strategies. This is the first report of a synthetic small molecule (GCTR) that effectively combats ferroptosis, simultaneously restoring enzymatic activity and enhancing cellular levels of its master regulator, GPX4. Further, GCTR disrupts Fe3+-induced LLPS of tau, and aids in attenuation of abnormal tau fibrillization. The synergistic action of GCTR in combating both ferroptosis and amyloid toxicity, bolstered by GPX4 enhancement and modulation of Fe3+-induced tau LLPS, holds promise for the development of small molecule-based novel therapeutics for AD.

Cooperative dissolution of peptidomimetic vesicles and amyloid β fibrils

The aggregation of amyloid proteins in the brain is a significant neurotoxic event that contributes to neurodegenerative disorders. The aggregation of amyloid beta (Aβ), particularly Aβ42 monomers, into various forms such as oligomers, protofibrils, fibrils, and amyloid plaques is a key pathological feature in Alzheimer's disease. As a result, Aβ42 is a primary target and the development of molecular strategies for the dissolution of Aβ42 aggregates is considered a promising approach to mitigating Alzheimer's disease pathology. A set of pyrene-conjugated peptidomimetics derived from Aβ14-23 (AkdcPy, AkdmPy, and AkdnPy) by incorporating an unnatural amino acid [kd: cyclo(Lys-Asp)] were studied for their ability to modulate Aβ42 aggregation. AkdcPy and AkdmPy formed vesicular structures in aqueous media. The vesicles of AkdmPy loaded with the neuroprotective compound berberine (Ber), dissipated mutually in the presence of preformed Aβ42 fibrils. During this process, the active drug Ber was released. This work is expected to inspire the development of drug-loaded peptidomimetic-based therapeutic formulations to modulate disorders associated with amyloid toxicity.

Mixed cyclo di-amino acids structured edible oils: a potential hardstock fat mimic

Pure cyclic diamino acids (CdAA) gel differently than combinations of CdAAs, altering the gelation behavior to highly-branched colloidal protein crystal networks reminiscent of traditional fat crystal networks in canola oil, making it an exciting structuring agent for unsaturated oils.

Effects of hydroxyl group in cyclo(Pro-Tyr)-like cyclic dipeptides on their anti-QS activity and self-assembly

We investigated the influence of hydroxyl groups on the anti-quorum-sensing (anti-QS) and anti-biofilm activity of structurally similar cyclic dipeptides, namely cyclo(L-Pro-L-Tyr), cyclo(L-Hyp-L-Tyr), and cyclo(L-Pro-L-Phe), against Pseudomonas aeruginosa PAO1. Cyclo(L-Pro-L-Phe), lacking hydroxyl groups, displayed higher virulence factor inhibition and cytotoxicity, but showed less inhibitory ability in biofilm formation. Cyclo(L-Pro-L-Tyr) and cyclo(L-Hyp-L-Tyr) suppressed genes in both the las and rhl systems, whereas cyclo(L-Pro-L-Phe) mainly downregulated rhlI and pqsR expression. These cyclic dipeptides interacted with the QS-related protein LasR, with similar binding efficiency to the autoinducer 3OC12-HSL, except for cyclo(L-Pro-L-Phe) which had lower affinity. In addition, the introduction of hydroxyl groups significantly improved the self-assembly ability of these peptides. Both cyclo(L-Pro-L-Tyr) and cyclo(L-Hyp-L-Tyr) formed assembly particles at the highest tested concentration. The findings revealed the structure-function relationship of this kind of cyclic dipeptides and provided basis for our follow-up research in the design and modification of anti-QS compounds.

Nanostructured Electrospun Fibers with Self-Assembled Cyclo-L-Tryptophan-L-Tyrosine Dipeptide as Piezoelectric Materials and Optical Second Harmonic Generators

The potential use of nanostructured dipeptide self-assemblies in materials science for energy harvesting devices is a highly sought-after area of research. Specifically, aromatic cyclo-dipeptides containing tryptophan have garnered attention due to their wide-bandgap semiconductor properties, high mechanical rigidity, photoluminescence, and nonlinear optical behavior. In this study, we present the development of a hybrid system comprising biopolymer electrospun fibers incorporated with the chiral cyclo-dipeptide L-Tryptophan-L-Tyrosine. The resulting nanofibers are wide-bandgap semiconductors (bandgap energy 4.0 eV) consisting of self-assembled nanotubes embedded within a polymer matrix, exhibiting intense blue photoluminescence. Moreover, the cyclo-dipeptide L-Tryptophan-L-Tyrosine incorporated into polycaprolactone nanofibers displays a strong effective second harmonic generation signal of 0.36 pm/V and shows notable piezoelectric properties with a high effective coefficient of 22 pCN-1, a piezoelectric voltage coefficient of geff=1.2 VmN-1 and a peak power density delivered by the nanofiber mat of 0.16μWcm-2. These hybrid systems hold great promise for applications in the field of nanoenergy harvesting and nanophotonics.

A Comprehensive Analysis of the Intrinsic Visible Fluorescence Emitted by Peptide/Protein Amyloid-like Assemblies

Amyloid aggregation is a widespread process that involves proteins and peptides with different molecular complexity and amino acid composition. The structural motif (cross-β) underlying this supramolecular organization generates aggregates endowed with special mechanical and spectroscopic properties with huge implications in biomedical and technological fields, including emerging precision medicine. The puzzling ability of these assemblies to emit intrinsic and label-free fluorescence in regions of the electromagnetic spectrum, such as visible and even infrared, usually considered to be forbidden in the polypeptide chain, has attracted interest for its many implications in both basic and applied science. Despite the interest in this phenomenon, the physical basis of its origin is still poorly understood. To gain a global view of the available information on this phenomenon, we here provide an exhaustive survey of the current literature in which original data on this fluorescence have been reported. The emitting systems have been classified in terms of their molecular complexity, amino acid composition, and physical state. Information about the wavelength of the radiation used for the excitation as well as the emission range/peak has also been retrieved. The data collected here provide a picture of the complexity of this multifaceted phenomenon that could be helpful for future studies aimed at defining its structural and electronic basis and/or stimulating new applications.

The Solvation Effect of C=O Group of Cyclic Anhydrides in Solution

The paper reports the results of investigation intermolecular interactions between alanine and sarcosine anhydride in organic solvents. The absorption frequencies of cyclic dipeptide in solvents were measured by IR spectroscopy. The effect of Van der Waals interactions and the hydrogen bonding of solvents on absorption frequencies of the C=O group of anhydrides was discussed. The spectroscopic parameters for C=O∙∙∙H-O hydrogen bonding complexes of anhydride with methanol in aprotic and proton donor solvent are obtained. In multi-particle complexes of dipeptides with aliphatic alcohols, the hydrogen bond enhancement was between 10 and 16%, which is significantly lower than it is for amide complexes.

Bioinspired Cyclic Dipeptide Functionalized Nanofibers for Thermal Sensing and Energy Harvesting

Nanostructured dipeptide self-assemblies exhibiting quantum confinement are of great interest due to their potential applications in the field of materials science as optoelectronic materials for energy harvesting devices. Cyclic dipeptides are an emerging outstanding group of ring-shaped dipeptides, which, because of multiple interactions, self-assemble in supramolecular structures with different morphologies showing quantum confinement and photoluminescence. Chiral cyclic dipeptides may also display piezoelectricity and pyroelectricity properties with potential applications in new sources of nano energy. Among those, aromatic cyclo-dipeptides containing the amino acid tryptophan are wide-band gap semiconductors displaying the high mechanical rigidity, photoluminescence and piezoelectric properties to be used in power generation. In this work, we report the fabrication of hybrid systems based on chiral cyclo-dipeptide L-Tryptophan-L-Tryptophan incorporated into biopolymer electrospun fibers. The micro/nanofibers contain self-assembled nano-spheres embedded into the polymer matrix, are wide-band gap semiconductors with 4.0 eV band gap energy, and display blue photoluminescence as well as relevant piezoelectric and pyroelectric properties with coefficients as high as 57 CN-1 and 35×10-6 Cm-2K-1, respectively. Therefore, the fabricated hybrid mats are promising systems for future thermal sensing and energy harvesting applications.

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

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

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

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

Nanotubes and water-channels from self-assembling dipeptides

Dipeptides are attractive building blocks for biomaterials in light of their inherent biocompatibility, biodegradability, and simplicity of preparation. Since the discovery of diphenylalanine (Phe-Phe) self-assembling ability into nanotubes, research efforts have been devoted towards the identification of other dipeptide sequences capable of forming these interesting nanomorphologies, although design rules towards nanotube formation are still elusive. In this review, we analyze the dipeptide sequences reported thus far for their ability to form nanotubes, which often feature water-filled supramolecular channels as revealed by single-crystal X-ray diffraction, as well as their properties, and their potential biological applications, which span from drug delivery and regenerative medicine, to bioelectronics and bioimaging.

Multifunctional Architectures of Cyclic Dipeptide Copolymers and Composites, and Modulation of Multifaceted Amyloid-β Toxicity

Alzheimer's disease (AD) is a major neurodegenerative disorder primarily characterized by the β-amyloid (Aβ42) misfolding and aggregation-associated multifaceted amyloid toxicity encompassing oxidative stress, neuronal death, and severe cognitive impairment. Modulation of Aβ42 aggregation via various structurally anisotropic macromolecular systems is considered effective in protecting neuronal cells. In this regard, we have developed a cyclic dipeptide (CDP)-based copolymer (CP) and explored its material and biomedical properties. Owing to the structural versatility, CDP-CP forms solvent-dependent anisotropic architectures ranging from dense fibers and mesosheets to vesicles, which are shown to interact with dyes and nanoparticles and mimic synthetic protocells, providing a conceptually new approach to achieve advanced functional materials with the hierarchical organization. CP upon interaction with gold nanoparticles (GNP) and polyoxometalate (POM) generated faceted architectures (CP-GNP) and the nanocomposite (CP-POM), respectively. CP-GNP and CP-POM have shown remarkable ability to inhibit Aβ42 aggregation, dissolve the preformed aggregates, and scavenge reactive oxygen species (ROS) to ameliorate multifaceted amyloid toxicity. In cellulo studies show that CP-GNP and CP-POM protect neuronal cells from Aβ42-induced toxicity and reduce lipopolysaccharide (LPS)-activated neuroinflammation at sub-micromolar concentration. To our knowledge, this is the first report on the hierarchical organization of CDP-CP into 1D-to-2D architectures and their organic-inorganic hybrid nanocomposites to combat the multifaceted amyloid toxicity.

Self-Assembly of Homo- and Hetero-Chiral Cyclodipeptides into Supramolecular Polymers towards Antimicrobial Gels

There is an increasing interest towards the development of new antimicrobial coatings, especially in light of the emergence of antimicrobial resistance (AMR) towards common antibiotics. Cyclodipeptides (CDPs) or diketopiperazines (DKPs) are attractive candidates for their ability to self-assemble into supramolecular polymers and yield gel coatings that do not persist in the environment. In this work, we compare the antimicrobial cyclo(Leu-Phe) with its heterochiral analogs cyclo(D-Leu-L-Phe) and cyclo(L-Leu-D-Phe), as well as cyclo(L-Phe-D-Phe), for their ability to gel. The compounds were synthesized, purified by HPLC, and characterized by ¹H-NMR, ¹³C-NMR, and ESI-MS. Single-crystal X-ray diffraction (XRD) revealed details of the intermolecular interactions within the supramolecular polymers. The DKPs were then tested for their cytocompatibility on fibroblast cells and for their antimicrobial activity on S. aureus. Overall, DKPs displayed good cytocompatibility and very mild antimicrobial activity, which requires improvement towards applications.

Imaging Orientation of a Single Molecular Hierarchical Self-Assembled Sheet: The Combined Power of a Vibrational Sum Frequency Generation Microscopy and Neural Network

In this work, we determined the tilt angles of molecular units in hierarchical self-assembled materials on a single-sheet level, which were not available previously. This was achieved by developing a fast line-scanning vibrational sum frequency generation (VSFG) hyperspectral imaging technique in combination with neural network analysis. Rapid VSFG imaging enabled polarization resolved images on a single sheet level to be measured quickly, circumventing technical challenges due to long-term optical instability. The polarization resolved hyperspectral images were then used to extract the supramolecular tilt angle of a self-assembly through a set of spectra-tilt angle relationships which were solved through neural network analysis. This unique combination of both novel techniques offers a new pathway to resolve molecular level structural information on self-assembled materials. Understanding these properties can further drive self-assembly design from a bottom-up approach for applications in biomimetic and drug delivery research.

Molecular Dynamics Investigation of Clustering in Aqueous Glycine Solutions

Recent experiments with undersaturated aqueous glycine solutions have repeatedly exhibited the presence of giant liquid-like clusters or nanodroplets around 100 nm in diameter. These nanodroplets re-appear even after careful efforts for their removal and purification of the glycine solution. The composition of these clusters is not clear, although it has been suggested that they are mainly composed of glycine, a small and very soluble amino acid. To gain insights into this phenomenon, we study the aggregation of glycine in aqueous solutions at concentrations below the experimental solubility limit using large-scale molecular dynamics simulations under ambient conditions. Three protonation states of glycine (zwitterion = GLZ, anion = GLA, and cation = GLC) are simulated using molecular force fields based on the 1.14*CM1A partial charge scheme, which incorporates the OPLS all-atom force field and TIP3P water. When initiated from dispersed states, we find that giant clusters do not form in our simulations unless salt impurities are present. Moreover, if simulations are initiated from giant cluster states, we find that they tend to dissolve in the absence of salt impurities. Therefore, the simulation results provide little support for the possibility that the giant clusters seen in experiments are composed purely of glycine (and water). Considering that strenuous efforts are made in experiments to remove impurities such as salt, we propose that the giant clusters observed might instead result from the aggregation of reaction products of aqueous glycine, such as diketopiperazine or other oligoglycines which may be difficult to separate from glycine using conventional methods, or their co-aggregation with glycine.

Self-Assembled Peptide Nanostructures for ECM Biomimicry

Proteins are functional building blocks of living organisms that exert a wide variety of functions, but their synthesis and industrial production can be cumbersome and expensive. By contrast, short peptides are very convenient to prepare at a low cost on a large scale, and their self-assembly into nanostructures and gels is a popular avenue for protein biomimicry. In this Review, we will analyze the last 5-year progress on the incorporation of bioactive motifs into self-assembling peptides to mimic functional proteins of the extracellular matrix (ECM) and guide cell fate inside hydrogel scaffolds.

One-pot synthesis of 2,5-diketopiperazine with high titer and versatility using adenylation enzyme

2,5-Diketopiperazine (DKP) is a cyclic peptide composed of two amino acids and has been recently reported to exhibit various biological activities. DKPs have been synthesized using various methods. In chemical synthesis, a multi-step reaction requiring purification and racemization is problematic. Although enzymatic synthesis can overcome these problems, there has been no example of a general-purpose synthesis of DKPs with high titers. Therefore, we propose a chemoenzymatic method that can synthesize DKPs in a general-purpose manner with high efficiency under mild conditions. The adenylation domain of tyrocidine synthetase A (TycA-A) catalyzes the adenylation reaction of amino acids, and various amides can be synthesized by a nucleophilic substitution reaction with any amine. On the other hand, DKPs can be produced via intramolecular cyclization reactions from dipeptide esters. Based on these observations, we expected a one-pot synthesis of DKPs via dipeptide ester synthesis by TycA-A and cyclization reactions. This method enabled the synthesis of more than 128 types of DKPs without racemization. Importantly, the intramolecular cyclization reaction proceeded largely depending on the pH. In particular, the cyclization reaction proceeded well in the pH range of 6.5-9.5. Based on these results, we constructed a bioreactor with pH-stat for purified enzyme reaction; cyclo(L-Trp-L-Pro) was produced at 4.07 mM by controlling the reaction pH over time using this reactor. The DKPs obtained using this method will provide deeper insights into their structures and functions in future studies. KEY POINTS: • Adenylation enzyme enabled one-pot synthesis of arbitrary 2,5-diketopiperazine. • Little or no racemization occurred during 2,5-diketopiperazine synthesis. • Bioreactor with pH-stat for purified enzymes improved the reaction rate.

Differential copper-guided architectures of amyloid β peptidomimetics modulate oxidation states and catalysis

Orchestration of differential architectures of designer peptidomimetics that modulate metal oxidation states to perform multiple chemical transformations remains a challenge. Cu-chelation and self-assembly properties of amyloid β (Aβ14-23) peptide were tuned by the incorporation of cyclic dipeptide (CDP) and pyrene (Py) as the assembly directing and reporting units, respectively. We explore the molecular architectonics of Aβ14-23 derived peptidomimetics (Akd^NMCPy) to form differential architectures that stabilize distinct Cu oxidation states. The fibrillar self-assembly of Akd^NMCPy is modulated to form nanosheets by the one-off addition of Cu^II. Notably, the serial addition of Cu^II resulted in the formation of micelle-like core-shell architectures. The micelle-like and nanosheet architectures were found to differentially stabilize Cu^II and Cu^I states and catalyze tandem oxidative-hydrolysis and alkyne-azide cycloaddition reactions, respectively.

S-Benzyl Cysteine Based Cyclic Dipeptide Super Hydrogelator: Enhancing Efficacy of an Anticancer Drug via Sustainable Release

Peptide based low molecular weight supramolecular hydrogels hold promising aspects in various fields of application especially in biomaterial and biomedical sciences such as drug delivery, wound healing, tissue engineering, cell proliferation, etc due to their extreme biocompatibility. Unlike linear peptides, cyclic peptides have more structural rigidity and tolerance to enzymatic degradation and high environmental stability which make them even better candidates for the above said applications. Herein, a new small cyclic dipeptide (CDP) cyclo-(Leu-S-Bzl-Cys) (P1) consisting of L-leucine and S-benzyl protected L-cysteine was reported which formed hydrogel at physiological conditions (at 37^o C and pH=7.46). The hydrogel formed from the cyclic dipeptide P1 showed very good tolerance towards environmental parameters such as pH, temperature and was seen to be stable for more than a year without any deformation. The hydrogel was thermoreversible and stable in the pH range 6-12. Mechanical strength of P1 hydrogel was measured by rheology experiment. AFM and FE-SEM images revealed that in aqueous solvents P1 self-assembled into a highly cross-linked nanofibrillar network which immobilized water molecules inside the cages and formed the hydrogel. The self-assembled cyclic dipeptide acquired antiparallel β-sheet secondary structure which was evident from CD and FT-IR studies. The β-sheet arrangement and formation of amyloid fibrils were further established by ThT binding assay. Furthermore, P1 was able to form hydrogel in presence of anticancer drug 5-fluorouracil (5FU) and sustainable release of the drug from the hydrogel was measured in-vitro. The hydrogelator P1 showed almost no cytotoxicity towards human colorectal cancer cell line HCT116 up to a considerable high concentration and showed potential application in sustainable drug delivery. The co-assembly of 5FU and P1 hydrogel exhibited much better anticancer activity towards HCT116 cancer cell line than 5-fluorouracil alone and decreased the IC₅₀ dose of 5-fluorouracil to a much lower value.

Efficient Hydro- and Organogelation by Minimalistic Diketopiperazines Containing a Highly Insoluble Aggregation-Induced, Blue-Shifted Emission Luminophore*

We report the synthesis, gelation abilities and aggregation‐induced, blue‐shifted emission (AIBSE) properties of two minimalistic diketopiperazine‐based gelators. Despite containing a highly insoluble luminophore that makes up more than half of their respective molecular masses, efficient hydrogelation by multiple stimuli for one and efficient organogelation for the other compound are reported. Insights into the aggregation and gelation properties were gained through examination of the photophysical and material properties of selected gels, which are representative of the different modes of gelation. The synthesis of the gelators is highly modular and based on readily available amino acid building blocks, allowing the efficient and rapid diversification of these core structures and fine‐tuning of gel properties.

Cyclic Dipeptides: The Biological and Structural Landscape with Special Focus on the Anti-Cancer Proline-Based Scaffold

Cyclic dipeptides, also know as diketopiperazines (DKP), the simplest cyclic forms of peptides widespread in nature, are unsurpassed in their structural and bio-functional diversity. DKPs, especially those containing proline, due to their unique features such as, inter alia, extra-rigid conformation, high resistance to enzyme degradation, increased cell permeability, and expandable ability to bind a diverse of targets with better affinity, have emerged in the last years as biologically pre-validated platforms for the drug discovery. Recent advances have revealed their enormous potential in the development of next-generation theranostics, smart delivery systems, and biomaterials. Here, we present an updated review on the biological and structural profile of these appealing biomolecules, with a particular emphasis on those with anticancer properties, since cancers are the main cause of death all over the world. Additionally, we provide a consideration on supramolecular structuring and synthons, based on the proline-based DKP privileged scaffold, for inspiration in the design of compound libraries in search of ideal ligands, innovative self-assembled nanomaterials, and bio-functional architectures.

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.

Cyclic Dipeptide: A Privileged Molecular Scaffold to Derive Structural Diversity and Functional Utility

Cyclic dipeptides (CDPs) are the simplest form of cyclic peptides with a wide range of applications from therapeutics to biomaterials. CDP is a versatile molecular platform endowed with unique properties such as conformational rigidity, intermolecular interactions, structural diversification through chemical synthesis, bioavailability and biocompatibility. A variety of natural products with the CDP core exhibit anticancer, antifungal, antibacterial, and antiviral activities. The inherent bioactivities have inspired the development of synthetic analogues as drug candidates and drug delivery systems. CDP plays a crucial role as conformation and molecular assembly directing core in the design of molecular receptors, peptidomimetics and fabrication of functional material architectures. In recent years, CDP has rapidly become a privileged scaffold for the design of advanced drug candidates, drug delivery agents, bioimaging, and biomaterials to mitigate numerous disease conditions. This review describes the structural diversification and multifarious biomedical applications of the CDP scaffold, discusses challenges, and provides future directions for the emerging field.

Diketopiperazine Gels: New Horizons from the Self-Assembly of Cyclic Dipeptides

Cyclodipeptides (CDPs) or 2,5-diketopiperazines (DKPs) can exert a variety of biological activities and display pronounced resistance against enzymatic hydrolysis as well as a propensity towards self-assembly into gels, relative to the linear-dipeptide counterparts. They have attracted great interest in a variety of fields spanning from functional materials to drug discovery. This concise review will analyze the latest advancements in their synthesis, self-assembly into gels, and their more innovative applications.

Molecular Architectonics-guided Design of Biomaterials

The quest for mastering the controlled engineering of dynamic molecular assemblies is the basis of molecular architectonics. The rational use of noncovalent interactions to programme the molecular assemblies allow the construction of diverse molecular and material architectures with novel functional properties and applications. Understanding and controlling the assembly of molecular systems are daunting tasks owing to the complex factors that govern at the molecular level. Molecular architectures depend on the design of functional molecular modules through the judicious selection of functional core and auxiliary units to guide the precise molecular assembly and co-assembly patterns. Biomolecules with built-in information for molecular recognition are the ultimate examples of evolutionary guided molecular recognition systems that define the structure and functions of living organisms. Explicit use of biomolecules as auxiliary units to command the molecular assemblies of functional molecules is an intriguing exercise in the scheme of molecular architectonics. In this minireview, we discuss the implementation of the principles of molecular architectonics for the development of novel biomaterials with functional properties and applications ranging from sensing, drug delivery to neurogeneration and tissue engineering. We present the molecular designs pioneered by our group owing to the requirement and scope of the article while acknowledging the designs pursued by several research groups that befit the concept.

Synthesis and solvent-controlled self-assembly of diketopiperazine-based polyamides from aspartame

An aspartame-based AB-type diketopiperazine monomer, cyclo(l-aspartyl-4-amino-l-phenylalanyl) (ADKP), was synthesized and subsequently utilized in the polycondensation of homo-polyamides with high molecular weights. By using various amino acids, dicarboxylic acids, and diamines, random DKP-based copolymers were also synthesized. The self-assembly properties of ADKP and poly(cyclo(l-aspartyl-4-amino-l-phenylalanyl)) (PA1) were studied via the solvent displacement method. Notably, PA1 self-assembled into particles with various morphologies in different solvent systems, such as irregular networks, ellipsoids, and hollow particles. The morphological transformation was also confirmed by dropping acetone and toluene onto the PA1 particles. Furthermore, infrared spectra and Hansen solubility parameters of PA1 and different solvents revealed the particle formation mechanism, which provided more insights into the relationship between the morphology and strength of the hydrogen bonding of each solvent.

Diketopiperazine-based polyamides have been synthesized from aspartame, and could self-assemble into particles with various morphologies in different solvents.

Recent advances in the fabrication and bio-medical applications of self-assembled dipeptide nanostructures

Molecular self-assembly is a widespread natural phenomenon and has inspired several researchers to synthesize a compendium of nano/microstructures with widespread applications. Biomolecules like proteins, peptides and lipids are used as building blocks to fabricate various nanomaterials. Supramolecular peptide self-assembly continue to play a significant role in forming diverse nanostructures with numerous biomedical applications; however, dipeptides offer distinctive supremacy in their ability to self-assemble and produce a variety of nanostructures. Though several reviews have articulated the progress in the field of longer peptides or polymers and their self-assembling behavior, there is a paucity of reviews or literature covering the emerging field of dipeptide-based nanostructures. In this review, our goal is to present the recent advancements in dipeptide-based nanostructures with their potential applications.

Self-Assembly of Cyclic Dipeptides: Platforms for Functional Materials

Supramolecular self-assembled functional materials comprised of cyclic dipeptide building blocks have excellent prospects for biotechnology applications due to their exceptional structural rigidity, morphological flexibility, ease of preparation and modification. Although the pharmacological uses of many natural cyclic dipeptides have been studied in detail, relatively little is reported on the engineering of these supramolecular architectures for the fabrication of functional materials. In this review, we discuss the progress in the design, synthesis, and characterization of cyclic dipeptide supramolecular nanomaterials over the past few decades, highlighting applications in biotechnology and optoelectronics engineering.

Co-solvent polarity tuned thermochromic nanotubes of cyclic dipeptide-polydiacetylene supramolecular system

The cooperative non-covalent interactions arising from structurally integrated multiple molecules have emerged as a powerful tool for the creation of functional supramolecular structures. Herein, we constructed cyclic dipeptide (CDP)–polydiacetylene (PDA) conjugate (CDP–DA) by introducing cyclo(l-Phe-l-Lys) to the linear 10,12-pentacosadiynoic acid. Owing to extensive hydrogen bonding characteristics, together with structural chirality of cyclo(l-Phe-l-Lys) and strong π–π stacking diacetylenic template, CDP–DA generated supramolecular nanotubes. The structural visualization using scanning and transmission electron microscopy revealed chloroform/methanol co-solvent polarity tuned morphological transformation of intrinsic lamellar assemblies into nanotubes comprising single-wall and multi-wall structure. The mechanistic understanding by X-ray diffraction patterns confirms bilayer organization in lamellar structure, which forms nanotubes via a gradual lamellar curling-to-scrolling process. The supramolecular CDP–DA nanotubes are transformed into the rigid covalently cross-linked blue-phase polydiacetylene (CDP–PDA) by UV irradiation. Very interestingly, the blue-phase nanotubes display reversible thermochromic changing temperature up to 150 °C with excellent repeatability over a dozen thermal cycles. This work provides an efficient strategy for precise morphological control and aiding the perspective for development in nanostructures for functional devices.

Co-solvent controlled fabrication of thermo-responsive chromogenic nanotubes of a cyclic dipeptide–polydiacetylene supramolecular system.

High-pressure studies on l,l-dileucine crystals by Raman spectroscopy and synchrotron X-ray diffraction combined with DFT calculations

The vibrational properties of the dipeptide l-leucyl-l-leucine hydrate were investigated through Raman and infrared spectroscopy. With the aid of first principle calculations using the density functional theory, the assignment of the vibrational modes from the material was furnished. In addition, the behavior of the crystal under high pressure was investigated using Raman spectroscopy (~8 GPa) and synchrotron X-ray diffraction (~26 GPa). The results show significant changes in both the X-ray diffractogram and the Raman spectra, suggesting that l-leucyl-l-leucine hydrate undergoes a phase transition between 2.3 and 2.9 GPa. Finally, for pressures above 16 GPa the broadening of X-ray peaks suggests a disorder in the crystal lattice induced by high-pressure effects.

A minimalistic hydrolase based on co-assembled cyclic dipeptides

The self-assembly of small peptides into larger aggregates is an important process for the fundamental understanding of abiogenesis. In this article we demonstrate that blends of cyclic dipeptides (2,5-diketopiperazines - DKPs) bearing either histidine or cysteine in combination with a lipophilic amino acid form highly stable aggregates in aqueous solution with esterase-like activity. We demonstrate that the catalytic activity is based on an intermolecular cooperative behavior between histidine and cysteine. A high control of the molecular arrangement of the peptide assemblies was gained by C-H-π interactions between Phe and Leu or Val sidechains, resulting in a significant increase in catalytic activity. These interactions were strongly supported by Hartree-Fock calculations and finally confirmed via1H-NMR HRMAS NOE spectroscopy.

Solid-state synthesis of cyclo LD-diphenylalanine: A chiral phase built from achiral subunits

The solid-state structure of LL/DD or LD/DL diphenylalanine diluted in KBr pellets is studied by infrared (IR) absorption and vibrational circular dichroism (VCD) spectroscopy. The structure depends on the absolute configuration of the residues. The natural LL diphenylalanine exists as a mixture of neutral and zwitterionic structures, depending on the humidity of the sample, while mostly the zwitterion is observed for LD diphenylalanine whatever the experimental conditions. The system undergoes spontaneous cyclization upon heating at 125°C, resulting to the formation of a diketopiperazine (DKP) dipeptide as the only product. The reaction is faster for LD than for LL diphenylalanine. As expected, LL and DD diphenylalanine react to form the LL and DD enantiomers of cyclo diphenylalanine. Interestingly, the DKP dipeptides formed from the LD or DL diphenylalanine show unexpected optical activity, with opposite VCD spectra for the products formed from the LD and DL reagents. This is explained in terms of chirality synchronization between the monomers within the crystal, which retain the symmetry of the reagent, resulting to the formation of a new chiral phase made from transiently chiral molecules.

A review on recent advances in polymer and peptide hydrogels

In this review, we focus on the very recent developments on the use of the stimuli responsive properties of polymer hydrogels for targeted drug delivery, tissue engineering, and biosensing utilizing their different optoelectronic properties. Besides, the stimuli-responsive hydrogels, the conducting polymer hydrogels are discussed, with specific attention to the energy generation and storage behavior of the xerogel derived from the hydrogel. The electronic and ionic conducting gels have been discussed that have applications in various electronic devices, e.g., organic field effect transistors, soft robotics, ionic skins, and sensors. The properties of polymer hybrid gels containing carbon nanomaterials have been exemplified here giving attention to applications in supercapacitors, dye sensitized solar cells, photocurrent switching, etc. Recent trends in the properties and applications of some natural polymer gels to produce thermal and acoustic insulating materials, drug delivery vehicles, self-healing material, tissue engineering, etc., are discussed. Besides the polymer gels, peptide gels of different dipeptides, tripeptides, oligopeptides, polypeptides, cyclic peptides, etc., are discussed, giving attention mainly to biosensing, bioimaging, and drug delivery applications. The properties of peptide-based hybrid hydrogels with polymers, nanoparticles, nucleotides, fullerene, etc., are discussed, giving specific attention to drug delivery, cell culture, bio-sensing, and bioimaging properties. Thus, the present review delineates, in short, the preparation, properties, and applications of different polymer and peptide hydrogels prepared in the past few years.

Thermally induced cyclization of L -isoleucyl-L -alanine in solid state: Effect of dipeptide structure on reaction temperature and self-assembly

Thermal treatment of short-chain oligopeptides is able to initiate the process of their self-assembly with the formation of organic nanostructures with unique properties. On the other hand, heating can lead to a chemical reaction with the formation of new substances with specific properties and ability to form structures with different morphology. Therefore, in order to have a desired process, researcher needs to find its temperature range. In the present work, cyclization of _L -isoleucyl-_L -alanine dipeptide in the solid state upon heating was studied. Kinetic parameters of this reaction were estimated within the approaches of the nonisothermal kinetics. The correlation between side chain structure of dipeptides and temperature of their cyclization in the solid state was found for the first time. This correlation may be used to predict the temperature, at which dipeptide self-assembly changes to chemical reaction. The differences in self-assembly of linear and cyclic dipeptides were demonstrated using atomic force microscopy. The effect of dipeptide concentration in a source solution and an organic solvent used on self-assembly of dipeptides was shown. The new information obtained on the thermal properties and self-assembly of linear and cyclic forms of _L -isoleucyl-_L -alanine may be useful for the design of new nanomaterials based on oligopeptides, as well as for the synthesis of cyclic oligopeptides.

Molecular motifs encoding self-assembly of peptide fibers into molecular gels

Peptides are a promising class of gelators, due to their structural simplicity, biocompatibility and versatility. Peptides were synthesized based on four amino acids: leucine, phenylalanine, tyrosine and tryptophan. These peptide gelators, with systematic structural variances in side chain structure and chain length, were investigated using Hansen solubility parameters to clarify molecular features that promote gelation in a wide array of solvents. It is of utmost importance to combine both changes to structural motifs and solvent in simultaneous studies to obtain a global perspective of molecular gelation. It was found that cyclization of symmetric dipeptides, into 2,5-diketopiperazines, drastically altered the gelation ability of the dipeptides. C-l-LL and C-l-YY, which are among the smallest peptide LMOGs reported to date, are robust gelators with a large radius of gelation (13.44 MPa^1/2 and 13.90 MPa^1/2, respectively), and even outperformed l-FF (5.61 MPa^1/2). Interestingly, both linear dipeptides (l-FF and l-LL) gelled similar solvents, yet when cyclized only cyclo-dityrosine was a robust gelator, while cyclo-diphenylalanine was not. Changes in the side chains drastically affected the crystal morphology of the resultant gels. Symmetric cyclo dipeptides of leucine and tyrosine were capable of forming extremely high aspect ratio fibers in numerous solvents, which represent new molecular motifs capable of driving self-assembly.