Cationic Side Chain Identity Directs the Hydrophobically Driven Self-Assembly of Amphiphilic β-Peptides in Aqueous Solution

Arginine-Rich Peptides Regulate the Pathogenic Galectin-10 Crystallization and Mitigate Crystallopathy-Associated Inflammation

Protein self-assembly into a crystal in vivo triggers acute or chronic organ injury that can lead to intractable diseases lacking specific treatment options. In this study, we report the discovery of ionic arginine-rich peptides to disrupt the pathogenic galectin-10 (gal-10) crystallization, where the aberrant deposition of gal-10 crystals in airways causes the activation of IL-1β-dependent inflammation and the stimulation of epithelial cells to produce TNF-α. Gal-10 crystals show susceptibility to pH changes and charged residue substitutions at the protein packing interfaces, manifesting the role of charge-charge attractions across protein-protein interaction interfaces in governing gal-10 crystallization. To dissolve the gal-10 crystal, the ionic peptides R9 and R12Y8 were identified to eliminate the interprotein charge-charge interactions. The efficacy of R12Y8 in mitigating the gal-10 crystallopathy in vivo was assessed in a crystal-induced lung inflammation mice model. The mice intratracheally administrated by R12Y8 exhibited a downregulated release of proinflammatory cytokines and reduced infiltration of inflammatory cells in the lungs. Our study demonstrates that the pathogenic gal-10 crystallization is readily eliminated by R-rich peptides, which may display translational potentials for the treatment of gal-10 crystallopathy.

Facile Reactive Oxygen Species-Scavenging Supramolecular Hydrogel to Promote Diabetic Wound Healing

Chronic wound healing impairment is a significant complication in diabetes. Hydrogels that maintain wound moisture and enable sustained drug release have become prominent for enhancing chronic wound care. Particularly, hydrogels that respond to reactive oxygen species (ROS) are sought-after for their dual capacity to mitigate ROS and facilitate controlled drug delivery at the wound site. We have strategically designed an ROS-responsive and scavenging supramolecular hydrogel composed of the simple hexapeptide Glu-Phe-Met-Phe-Met-Glu (EFM). This hydrogelator, composed solely of canonical amino acids without additional ROS-sensitive motifs, forms a hydrogel rapidly upon sonication. Interaction with ROS leads to the oxidation of Met residues to methionine sulfoxide, triggering hydrogel disassembly and consequent payload release. Cellular assays have verified their biocompatibility and efficacy in promoting cell proliferation and migration. In vivo investigations underscore the potential of this straightforward hydrogel as an ROS-scavenger and drug delivery vehicle, enhancing wound healing in diabetic mice. The simplicity and effectiveness of this hydrogel suggest its broader biomedical applications in the future.

β-Peptides incorporating polyhydroxylated cyclohexane β-amino acid: synthesis and conformational study

We describe the synthesis of trihydroxylated cyclohexane β-amino acids from (-)-shikimic acid, in their cis and trans configuration, and the incorporation of the trans isomer into a trans-2-aminocyclohexanecarboxylic acid peptide chain. Subsequently, the hydroxyl groups were partially or totally deprotected. The structural study of the new peptides by FTIR, CD, solution NMR and DFT calculations revealed that they all fold into a 14-helix secondary structure, similarly to the homooligomer of trans-2-aminocyclohexanecarboxylic acid. This means that the high degree of substitution of the cyclohexane ring of the new residue is compatible with the adoption of a stable helical secondary structure and opens opportunities for the design of more elaborate peptidic foldamers with oriented polar substituents at selected positions of the cycloalkane residues.

β-Sheet Assembly Translates Conservative Single-Site Mutation into a Perturbation in Macroscopic Structure

Transferring structural information from amino acid sequence to macroscale assembly is a challenging approach for designing protein quaternary structure. However, the pathway by which the slight variations in sequence result in a global perturbation effect on the assembled structure is unknown. Herein, we design two synthetic peptides, QNL-His and QNL-Arg, with one amino acid substitution and use scanning tunneling microscopy (STM) to image individual peptides in the assembled state. The submolecular resolution of STM enables us to determine the folding structure and β-sheet supramolecular organization of peptides. QNL-His and QNL-Arg differ in their β-strand length distribution in pleated β-sheet association. These structural variations lead to distinguishable outcomes in their β-sheet assembled fibrils and phase transitions. The comparison of QNL-His versus QNL-Arg structures and macroscopic properties unveils the role of assembly to amplify the structural variations associated with a single-site mutation from a single-molecule scale to a macroscopic scale.

Interactions of SARS-CoV-2 and MERS-CoV fusion peptides measured using single-molecule force methods

We address the challenge of understanding how hydrophobic interactions are encoded by fusion peptide (FP) sequences within coronavirus (CoV) spike proteins. Within the FPs of severe acute respiratory syndrome CoV 2 and Middle East respiratory syndrome CoV (MERS-CoV), a largely conserved peptide sequence called FP1 (SFIEDLLFNK and SAIEDLLFDK in SARS-2 and MERS, respectively) has been proposed to play a key role in encoding hydrophobic interactions that drive viral-host cell membrane fusion. Although a non-polar triad (Leu-Leu-Phe (LLF)) is common to both FP1 sequences, and thought to dominate the encoding of hydrophobic interactions, FP1 from SARS-2 and MERS differ in two residues (Phe 2 versus Ala 2 and Asn 9 versus Asp 9, respectively). Here we explore whether single-molecule force measurements can quantify hydrophobic interactions encoded by FP1 sequences, and then ask whether sequence variations between FP1 from SARS-2 and MERS lead to significant differences in hydrophobic interactions. We find that both SARS-2 and MERS wild-type FP1 generate measurable hydrophobic interactions at the single-molecule level, but that SARS-2 FP1 encodes a substantially stronger hydrophobic interaction than its MERS counterpart (1.91 ± 0.03 nN versus 0.68 ± 0.03 nN, respectively). By performing force measurements with FP1 sequences with single amino acid substitutions, we determine that a single-residue mutation (Phe 2 versus Ala 2) causes the almost threefold difference in the hydrophobic interaction strength generated by the FP1 of SARS-2 versus MERS, despite the presence of LLF in both sequences. Infrared spectroscopy and circular dichroism measurements support the proposal that the outsized influence of Phe 2 versus Ala 2 on the hydrophobic interaction arises from variation in the secondary structure adopted by FP1. Overall, these insights reveal how single-residue diversity in viral FPs, including FP1 of SARS-CoV-2 and MERS-CoV, can lead to substantial changes in intermolecular interactions proposed to play a key role in viral fusion, and hint at strategies for regulating hydrophobic interactions of peptides in a range of contexts.

Advances in hybrid peptide-based self-assembly systems and their applications

Self-assembly of peptides demonstrates a great potential for designing highly ordered, finely tailored supramolecular arrangements enriched with high specificity, improved efficacy and biological activity. Along with natural peptides, hybrid peptide systems composed of natural and chemically diverse unnatural amino acids have been used in various fields, including drug delivery, wound healing, potent inhibition of diseases, and prevention of biomaterial related diseases to name a few. In this review, we provide a brief outline of various methods that have been utilized for obtaining fascinating structures that create an avenue to reproduce a range of functions resulting from these folds. An overview of different self-assembled structures as well as their applications will also be provided. We believe that this review is very relevant to the current scenario and will cover conformations of hybrid peptides and resulting self-assemblies from the late 20^th century through 2022. This review aims to be a comprehensive and reliable account of the hybrid peptide-based self-assembly owing to its enormous influence in understanding and mimicking biological processes.

Peptide Binder with High-Affinity for the SARS-CoV-2 Spike Receptor-Binding Domain

Rapid antigen detection tests are urgently needed for the early diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The discovery of a binder with high affinity and selectivity for the biomarkers presented by SARS-CoV-2 is crucial to the development of the rapid antigen detection method. We utilized the surface biopanning to identify a peptide binder R1 from a phage-displayed peptide library consisting of 109 independent phage recombinants. The R1 peptide exhibited high-affinity for specific binding with the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with a dissociation constant KD of (7.5 ± 1.9) × 10-10 M, which maintained high binding affinity with the RBD derived from Gamma, Lambda, Delta, and Omicron variants. The composition and sequence dependence of binding characteristics in R1-RBD interactions was revealed by the binding affinity fluctuations between RBD and the scrambled sequences or single-site mutants of R1. The R1-functionalized gold nanoparticles possessed concentration-dependent response to RBD and selectivity over bovine serum albumin and human serum albumin. The peptide binder R1 shows the potential to be used for constructing a rapid detection method for the early-stage diagnostics for SARS-CoV-2.

Perturbation effect of single polar group substitution on the Self-Association of amphiphilic peptide helices

As an important attempt towards creating hierarchical structures more like nature, the peptide is employed as a building block to build supramolecular architectures. An emerging question is whether the molecular mechanism of self-assembly obtained from the small molecule system, e.g., the driving forces of assembly are conventionally regarded as pairwise-additive, can be manifested in the self-association of biologically relevant amphiphilic peptides. A peptide, KRT-R, was derived from the 120-144 segment of keratin 14. The single cation-to-cation substitution with KRT-R at the site of 125 from arginine (R) to either lysine (K) or histidine (H) results in the peptide helices, KRT-K and KRT-H, sharing 96% sequence identity. These KRT-derived peptides possess similarities in the folding structures but exhibit divergent self-assembled structures. KRT-R and KRT-K self-assemble into sheets and fibrils, respectively. Whereas KRT-H associates into heterogeneous structures, including sheets, particles, and branched networks. The intrinsic tyrosine fluorescence spectroscopy measurements with the KRT-derived peptides within a temperature range of 25 °C to 95 °C reveal that the heating-triggered structural transitions of KRT-derived peptides are divergent. The alternation of single cationic residue changes the thermodynamic signature of peptide assemblies upon heating. A chemical denaturation experiment with KRT-derived peptides indicates that the intermolecular interactions that govern the supramolecular architectures formed by peptides are distinct. Overall, our work demonstrates the contribution of the interplay among various noncovalent interactions to supramolecular assembly.

Ultrasound-Induced Amino Acid-Based Hydrogels With Superior Mechanical Strength for Controllable Long-Term Release of Anti-Cercariae Drug

Stimulus-responsive hydrogels are significantly programmable materials that show potential applications in the field of biomedicine and the environment. Ultrasound as a stimulus can induce the formation of hydrogels, which exhibit the superior performance of different structures. In this study, we reported an ultrasound-induced supramolecular hydrogel based on aspartic acid derivative N,N'-diaspartate-3,4,9,10-perylene tetracarboxylic acid imide, showing superior performance in drug release. The results show that the driving force of this ultrasonic induced hydrogel could be attributed to hydrogen bonding and π-π interaction. The rheological and cytotoxicity test illustrate excellent mechanical properties and biocompatibility of the hydrogel. The anti-Schistosoma japonicum cercariae (CC) drug release results show large drug loadings (500 mg/ml) and long-term release (15 days) of this hydrogel. This study demonstrates that this hydrogel may serve as a slow-release platform for anti-CC.

Conservation and Identity Selection of Cationic Residues Flanking the Hydrophobic Regions in Intermediate Filament Superfamily

The interplay between the hydrophobic interactions generated by the nonpolar region and the proximal functional groups within nanometers of the nonpolar region offers a promising strategy to manipulate the intermolecular hydrophobic attractions in an artificial molecule system, but the outcomes of such modulations in the building of a native protein architecture remain unclear. Here we focus on the intermediate filament (IF) coiled-coil superfamily to assess the conservation of positively charged residue identity via a biostatistical approach. By screening the disease-correlated mutations throughout the IF superfamily, 10 distinct hotspots where a cation-to-cation substitution is associated with a pathogenic syndrome have been identified. The analysis of the local chemical context surrounding the hotspots revealed that the cationic diversity depends on their separation distance to the hydrophobic domain. The nearby cationic residues flanking the hydrophobic domain of a helix (separation <1 nm) are relatively conserved in evolution. In contrast, the cationic residues that are not adjacent to the hydrophobic domain (separation >1 nm) tolerate higher levels of variation and replaceability. We attribute this bias in the conservation degree of the cationic residue identity to reflect the interplay between the proximal cations and the hydrophobic interactions.

Rational Biological Interface Engineering: Amyloidal Supramolecular Microstructure-Inspired Hydrogel

Amyloidal proteins, which are prone to form fibrillar and ordered aggregates in vivo and in vitro, underlie the mechanism for neurodegenerative disorders and also play essential functions in the process of life. Amyloid fibrils typically adopt a distinctive β-sheet structure, which renders them with inherent extracellular matrix (ECM)-mimicking properties, such as powerful mechanical strength, promising adhesion, and antibacterial activity. Additionally, amyloidal proteins are a category of programmable self-assembled macromolecules, and their assembly and consequent nanostructure can be manipulated rationally. The above advantages motivate researchers to investigate the potential of amyloidal proteins as a novel type of hydrogel material. Currently, the amyloid-inspired hydrogel has become an emerging area and has been widely applied in a variety of biomedical fields, such as tissue repair, cell scaffolds, and drug delivery. In this review, we focus on the discussion of molecular mechanisms underlying the hydrogenation of amyloidal proteins, and introduce the advances achieved in biomedical applications of amyloid-inspired hydrogels.

Current Strategies for Microbubble-Based Thrombus Targeting: Activation-Specific Epitopes and Small Molecular Ligands

Microbubbles with enhanced ultrasound represent a potentially potent evolution to the administration of a free drug in the treatment of thrombotic diseases. Conformational and expressional changes of several thrombotic biological components during active coagulation provide epitopes that allow site-specific delivery of microbubble-based agents to the thrombus for theranostic purpose. Through the interaction with these epitopes, emerging high-affinity small molecular ligands are able to selectively target the thrombi with tremendous advantages over traditional antibody-based strategy. In this mini-review, we summarize recent novel strategies for microbubble-based targeting of thrombus through epitopes located at activated platelets and fibrin. We also discuss the challenges of current targeting modalities and supramolecular carrier systems for their translational use in thrombotic pathologies.

Peptide-Enabled Targeted Delivery Systems for Therapeutic Applications

Receptor-targeting peptides have been extensively pursued for improving binding specificity and effective accumulation of drugs at the site of interest, and have remained challenging for extensive research efforts relating to chemotherapy in cancer treatments. By chemically linking a ligand of interest to drug-loaded nanocarriers, active targeting systems could be constructed. Peptide-functionalized nanostructures have been extensively pursued for biomedical applications, including drug delivery, biological imaging, liquid biopsy, and targeted therapies, and widely recognized as candidates of novel therapeutics due to their high specificity, well biocompatibility, and easy availability. We will endeavor to review a variety of strategies that have been demonstrated for improving receptor-specificity of the drug-loaded nanoscale structures using peptide ligands targeting tumor-related receptors. The effort could illustrate that the synergism of nano-sized structures with receptor-targeting peptides could lead to enrichment of biofunctions of nanostructures.

Opposite Regulatory Effects of Immobilized Cations on the Folding Vs. Assembly of Melittin

Ions are crucial in modulating the protein structure. For the free ions in bulk solution, ammonium is kosmotropic (structure forming) and guanidinium is chaotropic (structure breaking) to the protein structure within the Hofmeister series. However, the effect of immobilized ions on a protein surface is less explored. Herein, we explored the influence of two immobilized cations (ammonium in the side chain of lysine and guanidinium in the side chain of arginine) on the folding and assembly of melittin. Melittin adopts an α-helix structure and is driven by hydrophobic interactions to associate into a helical bundle. To test the influence of immobilized cations on the peptide structure, we designed the homozygous mutants exclusively containing ammonium (melittin-K) or guanidinium (melittin-R) and compared the differences of melittin-K vs. melittin-R in their folding, assembly, and molecular functions. The side chains of lysine and arginine differ in their influences on the folding and assembly of melittin. Specifically, the side chain of R increases the α-helical propensity of melittin relative to that of K, following an inverse Hofmeister series. In contrast, the side chain of K favors the assembly of melittin relative to the side chain of R in line with a direct Hofmeister series. The opposite regulatory effects of immobilized cations on the folding and assembly of melittin highlight the complexity of the noncovalent interactions that govern protein intermolecular architecture.

A minireview on the perturbation effects of polar groups to direct nanoscale hydrophobic interaction and amphiphilic peptide assembly

Hydrophobic interaction provides the essential driving force for creating diverse native and artificial supramolecular architectures. Accumulating evidence leads to a hypothesis that the hydrophobicity of a nonpolar patch of a molecule is non-additive and susceptible to the chemical context of a judicious polar patch. However, the quantification of the hydrophobic interaction at the nanoscale remains a central challenge to validate the hypothesis. In this review, we aim to outline the recent efforts made to determine the hydrophobic interaction at a nanoscopic length scale. The advances achieved in the understanding of proximal polar groups perturbing the magnitude of hydrophobic interaction generated by the nonpolar patch are introduced. We will also discuss the influence of chemical heterogeneity on the modulation of amphiphilic peptide/protein assembly and molecular recognition.

Hydrophobic interaction provides the essential driving force for creating diverse native and artificial supramolecular architectures.