Biocatalysis of D,L-Peptide Nanofibrillar Hydrogel

Design Strategy of PepNzymes-SH for an Emerging Catalyst with Serine Hydrolase-Like Functionality

Serine hydrolases, as a class of green catalysts with hydrolytic and dehydrating activities, hold significant application value in the fields of biosynthesis and organic synthesis. However, practical applications face numerous challenges, including maintaining enzyme stability and managing usage costs. PepNzymes-SH, an emerging green catalytic material with enzyme-like activity, overcomes the operational limitations of natural enzymes and holds great promise as a substitute for hydrolases. Unfortunately, a systematic review of the design strategies for PepNzymes-SH is currently lacking. The core significance of this report lies in providing researchers with a comprehensive understanding and theoretical guidance through the summarization and performance evaluation of different design strategies of PepNzymes-SH. This review summarizes strategies for simulating and enhancing the stability of serine hydrolase active sites, oxyanion holes, and hydrophobic environmental structures. By comparing their catalytic activities, we assess the performance changes brought about by different strategies. Furthermore, the applications of PepNzymes-SH in the chemical, biomedicine, and environmental fields are also discussed.

Peptide Sequence Variations Govern Hydrogel Stiffness: Insights from a Multi-Scale Structural Analysis of H-FQFQFK-NH2 Peptide Derivatives

Throughout the past decades, amphipathic peptide-based hydrogels have proven to be promising materials for biomedical applications. Amphipathic peptides are known to adopt β-sheet configurations that self-assemble into fibers that then interact to form a hydrogel network. A fundamental understanding of how the peptide sequence alters the structural properties of the hydrogels would allow for a more rational design of novel peptides for a variety of biomedical applications in the future. Therefore, the current work investigates how changing the type of amino acid, the amphipathic pattern, and the peptide length affects the secondary structure, fiber characteristics, and stiffness of peptide-based hydrogels. Hereto, seven amphipathic peptides of different sequence and length, four of which have not been previously reported, based on and including the hexapeptide H-Phe-Gln-Phe-Gln-Phe-Lys-NH2, are synthesized and thoroughly characterized by circular dichroism (CD), Fourier Transform Infrared (FTIR) spectroscopy, Wide Angle X-ray Scattering (WAXS), Small Angle X-ray Scattering (SAXS), Transmission Electron Microscopy (TEM), and Thioflavin T (ThT) fibrillization assays. The results show that a high amount of regularly spaced β-sheets, a high amount of fibers, and fiber bundling contribute to the stiffness of the hydrogel. Furthermore, a study of the time-dependent fibril formation process reveals complex transient dynamics. The peptide strands structure through an intermediate helical state prior to β-sheet formation, which is found to be concentration- and time-dependent.

Determining the esterase activity of peptides and peptide assemblies

Catalytic peptides are gaining attention as alternatives to enzymes, especially in industrial applications. Recent advances in peptide design have improved their catalytic efficiency with approaches such as self-assembly and metal ion complexation. However, the fundamental principles governing peptide catalysis at the sequence level are still being explored. Ester hydrolysis, a well-studied reaction, serves as a widely employed method to evaluate the catalytic potential of peptides. The standard colorimetric reaction involving para-nitrophenyl acetate hydrolysis acts as a benchmark assay, providing a straightforward and efficient screening method for rapidly identifying potential catalysts. However, maintaining standardized conditions is crucial for reproducible results, given that factors such as pH, temperature, and substrate concentration can introduce unwanted variability. This necessity becomes particularly pronounced when working with peptides, which often exhibit slower reaction rates compared to enzymes, making even minor variations significantly influential on the final outcome. In this context, we present a refined protocol for assessing the catalytic activity of peptides and peptide assemblies, addressing critical considerations for reproducibility and accuracy.

Short Peptides for Hydrolase Supramolecular Mimicry and Their Potential Applications

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

Manually curated dataset of catalytic peptides for ester hydrolysis

Catalytic peptides are low cost biomolecules able to catalyse chemical reactions such as ester hydrolysis. This dataset provides a list of catalytic peptides currently reported in literature. Several parameters were evaluated, including sequence length, composition, net charge, isoelectric point, hydrophobicity, self-assembly propensity and mechanism of catalysis. Along with the analysis of physico-chemical properties, the SMILES representation for each sequence was generated to provide an easy-to-use means of training machine learning models. This offers a unique opportunity for the development and validation of proof-of-concept predictive models. Being a reliable manually curated dataset, it also enables the benchmark for comparison of new models or models trained on automatically gathered peptide-oriented datasets. Moreover, the dataset provides an insight in the currently developed catalytic mechanisms and can be used as the foundation for the development of next-generation peptide-based catalysts.

Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs

Ester hydrolysis is of wide biomedical interest, spanning from the green synthesis of pharmaceuticals to biomaterials' development. Existing peptide-based catalysts exhibit low catalytic efficiency compared to natural enzymes, due to the conformational heterogeneity of peptides. Moreover, there is lack of understanding of the correlation between the primary sequence and catalytic function. For this purpose, we statistically analyzed 22 EC 3.1 hydrolases with known catalytic triads, characterized by unique and well-defined mechanisms. The aim was to identify patterns at the sequence level that will better inform the creation of short peptides containing important information for catalysis, based on the catalytic triad, oxyanion holes and the triad residues microenvironments. Moreover, fragmentation schemes of the primary sequence of selected enzymes alongside the study of their amino acid frequencies, composition, and physicochemical properties are proposed. The results showed highly conserved catalytic sites with distinct positional patterns and chemical microenvironments that favor catalysis and revealed variations in catalytic site composition that could be useful for the design of minimalistic catalysts.

Catalytically Active Amyloids as Future Bionanomaterials

Peptides and proteins can aggregate into highly ordered and structured conformations called amyloids. These supramolecular structures generally have convergent features, such as the formation of intermolecular beta sheets, that lead to fibrillary architectures. The resulting fibrils have unique mechanical properties that can be exploited to develop novel nanomaterials. In recent years, sequences of small peptides have been rationally designed to self-assemble into amyloids that catalyze several chemical reactions. These amyloids exhibit reactive surfaces that can mimic the active sites of enzymes. In this review, I provide a state-of-the-art summary of the development of catalytically active amyloids. I will focus especially on catalytic activities mediated by hydrolysis, which are the most studied examples to date, as well as novel types of recently reported activities that promise to expand the possible repertoires. The combination of mechanical properties with catalytic activity in an amyloid scaffold has great potential for the development of future bionanomaterials aimed at specific applications.

Fabrication of injectable hydrogels from an anticancer peptide for local therapeutic delivery and synergistic photothermal-chemotherapy

The susceptibility of anticancer peptides to proteolytic degradation is often considered as a major weakness that limits systemic therapeutic applications. However, localized delivery of anticancer peptides via injectable hydrogels is expected to improve drug efficacy and reduce systemic toxicity. Herein, an injectable hydrogel with drug releasing properties, NIR responsiveness and pH sensitivity was developed from an anticancer peptide (KL), Fe³⁺ ions and protocatechualdehyde via dynamic and reversible interactions. Benefiting from the formation of Fe(III)-catechol complexes between Fe³⁺ ions and protocatechualdehyde within gel networks, the obtained hydrogel exhibited intrinsic NIR absorption properties for photothermal ablation of tumor cells, and remote light control of drug release. Besides, the pH-labile imine bonds between KL and protocatechualdehyde endowed the injectable gel with pH sensitivity for sustained release of KL under a mildly acidic environment, inducing membrane destabilization and facilitating the cell uptake of DOX for combinational chemotherapy. Both in vitro and in vivo experiments revealed that the injectable hydrogel exhibited a synergistic therapeutic effect on inhibiting tumor growth via combinational photothermal-chemotherapy. Therefore, this work provides a promising attempt to develop a therapeutic hydrogel from an anticancer peptide, which could work as a localized drug delivery platform for synergistic photothermal-chemotherapy.

Supramolecular assemblies of histidine-containing peptides with switchable hydrolase and peroxidase activities through Cu(II) binding and co-assembling

Modulating enzyme activities or functionalities is one of the primary features of biological systems, which is, however, a great challenge for artificial enzyme systems. In this work, we designed and synthesized a series of self-assembling peptides from histidine and other amino acids (Asp, Ser, Lys or Arg), which exist in the active site of natural enzymes. These peptides could undergo a conformational transition from random coils to β-sheet structures under physiological conditions and formed self-assembled nanotubes with obvious hydrolase activities. After incorporation of transition metal ions such as Cu²⁺, these peptides could coordinate with Cu²⁺ ions, switch molecular conformations, and self-assemble into hybrid nanomaterials with altered morphologies and peroxidase-like activities. This work illustrates a facile approach for constructing artificial enzymes from self-assembling peptides with histidine residues whose catalytic functions could be modulated by incorporation of Cu²⁺ ions.

Biological Functions and Applications of Antimicrobial Peptides

Abstract:

Despite antimicrobial resistance, which is attributed to the misuse of broad-spectrum antibiotics, antibiotics can indiscriminately kill pathogenic and beneficial microorganisms. These events disrupt the delicate microbial balance in both humans and animals, leading to secondary infections and other negative effects. Antimicrobial peptides (AMPs) are functional natural biopolymers in plants and animals. Due to their excellent antimicrobial activities and absence of microbial resistance, AMPs have attracted enormous research attention. We reviewed the antibacterial, antifungal, antiviral, antiparasitic, as well as antitumor properties of AMPs and research progress on AMPs. In addition, we highlighted various recommendations and potential research areas for their progress and challenges in practical applications.

Amyloids as Building Blocks for Macroscopic Functional Materials: Designs, Applications and Challenges

Amyloids are self-assembled protein aggregates that take cross-β fibrillar morphology. Although some amyloid proteins are best known for their association with Alzheimer’s and Parkinson’s disease, many other amyloids are found across diverse organisms, from bacteria to humans, and they play vital functional roles. The rigidity, chemical stability, high aspect ratio, and sequence programmability of amyloid fibrils have made them attractive candidates for functional materials with applications in environmental sciences, material engineering, and translational medicines. This review focuses on recent advances in fabricating various types of macroscopic functional amyloid materials. We discuss different design strategies for the fabrication of amyloid hydrogels, high-strength materials, composite materials, responsive materials, extracellular matrix mimics, conductive materials, and catalytic materials.

Heterochiral tetrapeptide self-assembly into hydrogel biomaterials for hydrolase mimicry

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

Tripeptide Self-Assembly into Bioactive Hydrogels: Effects of Terminus Modification on Biocatalysis

Bioactive hydrogels based on the self-assembly of tripeptides have attracted great interest in recent years. In particular, the search is active for sequences that are able to mimic enzymes when they are self-organized in a nanostructured hydrogel, so as to provide a smart catalytic (bio)material whose activity can be switched on/off with assembly/disassembly. Within the diverse enzymes that have been targeted for mimicry, hydrolases find wide application in biomaterials, ranging from their use to convert prodrugs into active compounds to their ability to work in reverse and catalyze a plethora of reactions. We recently reported the minimalistic l-His-d-Phe-d-Phe for its ability to self-organize into thermoreversible and biocatalytic hydrogels for esterase mimicry. In this work, we analyze the effects of terminus modifications that mimic the inclusion of the tripeptide in a longer sequence. Therefore, three analogues, i.e., N-acetylated, C-amidated, or both, were synthesized, purified, characterized by several techniques, and probed for self-assembly, hydrogelation, and esterase-like biocatalysis. This work provides useful insights into how chemical modifications at the termini affect self-assembly into biocatalytic hydrogels, and these data may become useful for the future design of supramolecular catalysts for enhanced performance.