Controlling Supramolecular Fiber Formation of Nucleopeptide by Guanosine Triphosphate.

Cells use dynamic self-assembly to construct functional structures for maintaining cellular homeostasis. However, using a natural biological small molecule to mimic this phenomenon remains challenging. This work reports the dynamic microfiber formation of nucleopeptide driven by guanosine triphosphate, the small molecule that controls microtubule polymerization in living cells. Deactivation of GTP by enzyme dissociates the fibers, which could be reactivated by adding GTP. Molecular dynamic simulation unveils the mystery of microfiber formation of GBM-1 and GTP. Moreover, the microfiber formation can also be controlled by diffusion-driven GTP gradients across a semipermeable membrane in bulk conditions and the microfluidic method in the defined droplets. This study provides a new platform to construct dynamic self-assembly materials of molecular building blocks driven by GTP.

Surface-Induced Hydrogelation for Fluorescence and Naked-Eye Detections of Enzyme Activity in Blood.

Fluorescence probes have been widely applied for the detection of important analytes with high sensitivity and specificity. However, they cannot be directly applied for the detection in samples with autofluorescence such as blood. Herein, we demonstrated a simple but effective method of surface-induced self-assembly/hydrogelation for fluorescence detection of an enzyme in biological fluids including blood and cell lysates. The method utilizes an attracting glass surface to induce self-assembly of an enzyme-generating fluorescent probe. After removing the upper solution, the fluorescence turn-on at the glass surface can therefore be used for the detection of enzyme activity. By judging the thickness and color depth of hydrogels at the surface of the glass plates, we could also estimate the enzyme activity by naked eyes. Our study not only expands the application of molecular self-assembly but also provides a useful method that can be applied for direct detection of enzyme activity in complex biological samples such as blood and cell lysates.

Deep Learning Empowers the Discovery of Self-Assembling Peptides with Over 10 Trillion Sequences.

Self-assembling of peptides is essential for a variety of biological and medical applications. However, it is challenging to investigate the self-assembling properties of peptides within the complete sequence space due to the enormous sequence quantities. Here, it is demonstrated that a transformer-based deep learning model is effective in predicting the aggregation propensity (AP) of peptide systems, even for decapeptide and mixed-pentapeptide systems with over 10 trillion sequence quantities. Based on the predicted AP values, not only the aggregation laws for designing self-assembling peptides are derived, but the transferability relation among the APs of pentapeptides, decapeptides, and mixed pentapeptides is also revealed, leading to discoveries of self-assembling peptides by concatenating or mixing, as consolidated by experiments. This deep learning approach enables speedy, accurate, and thorough search and design of self-assembling peptides within the complete sequence space of oligopeptides, advancing peptide science by inspiring new biological and medical applications.

Accelerating the prediction and discovery of peptide hydrogels with human-in-the-loop.

The amino acid sequences of peptides determine their self-assembling properties. Accurate prediction of peptidic hydrogel formation, however, remains a challenging task. This work describes an interactive approach involving the mutual information exchange between experiment and machine learning for robust prediction and design of (tetra)peptide hydrogels. We chemically synthesize more than 160 natural tetrapeptides and evaluate their hydrogel-forming ability, and then employ machine learning-experiment iterative loops to improve the accuracy of the gelation prediction. We construct a score function coupling the aggregation propensity, hydrophobicity, and gelation corrector Cg, and generate an 8,000-sequence library, within which the success rate of predicting hydrogel formation reaches 87.1%. Notably, the de novo-designed peptide hydrogel selected from this work boosts the immune response of the receptor binding domain of SARS-CoV-2 in the mice model. Our approach taps into the potential of machine learning for predicting peptide hydrogelator and significantly expands the scope of natural peptide hydrogels.

Retinal Microenvironment-Protected Rhein-GFFYE Nanofibers Attenuate Retinal Ischemia-Reperfusion Injury via Inhibiting Oxidative Stress and Regulating Microglial/Macrophage M1/M2 Polarization.

Retinal ischemia is involved in the occurrence and development of various eye diseases, including glaucoma, diabetic retinopathy, and central retinal artery occlusion. To the best of our knowledge, few studies have reported self-assembling peptide natural products for the suppression of ocular inflammation and oxidative stress. Herein, a self-assembling peptide GFFYE is designed and synthesized, which can transform the non-hydrophilicity of rhein into an amphiphilic sustained-release therapeutic agent, and rhein-based therapeutic nanofibers (abbreviated as Rh-GFFYE) are constructed for the treatment of retinal ischemia-reperfusion (RIR) injury. Rh-GFFYE significantly ameliorates oxidative stress and inflammation in an in vitro oxygen-glucose deprivation (OGD) model of retinal ischemia and a rat model of RIR injury. Rh-GFFYE also significantly enhances retinal electrophysiological recovery and exhibits good biocompatibility. Importantly, Rh-GFFYE also promotes the transition of M1-type macrophages to the M2 type, ultimately altering the pro-inflammatory microenvironment. Further investigation of the treatment mechanism indicates that Rh-GFFYE activates the PI3K/AKT/mTOR signaling pathway to reduce oxidative stress and inhibits the NF-κB and STAT3 signaling pathways to affect inflammation and macrophage polarization. In conclusion, the rhein-loaded nanoplatform alleviates RIR injury by modulating the retinal microenvironment. The findings are expected to promote the clinical application of hydrophobic natural products in RIR injury-associated eye diseases.

Self-assembled peptides-modified flexible field-effect transistors for tyrosinase detection.

Flexible biosensors have received intensive attention for real-time, non-invasive monitoring of cancer biomarkers. Highly sensitive tyrosinase biosensors, which are important for melanoma screening, remained a hurdle. Herein, high-performance tyrosinase-sensing field-effect transistor-based biosensors (bio-FETs) have been successfully achieved by self-assembling nanostructured tetrapeptide tryptophan-valine-phenylalanine-tyrosine (WVFY) on n-type metal oxide transistors. In the presence of target tyrosinase, the phenolic hydroxyl groups in WVFY are rapidly converted to benzoquinone with the consumption of protons, which could be detected potentiometrically by bio-FETs. As a result, the WVFY-modified bio-FETs exhibited an ultra-low detection limit of 1.9 fM and an optimal detection range of 10 fM to 1 nM toward tyrosinase sensing. Furthermore, flexible devices fabricated on ∼2.9-µm-thick polyimide (PI) substrates illustrated robust mechanical flexibility, which could be attached to human skin conformally. These achievements hold promise for wearable melanoma screening and provide designing guidelines for detecting other important cancer biomarkers with bio-FETs.

Encapsulation of LXR ligand by D-Nap-GFFY hydrogel enhances anti-tumorigenic actions of LXR and removes LXR-induced lipogenesis.

Background and purpose: Activation of liver X receptor (LXR) by its ligand T0901317 (T317) enhances interferon-γ (IFNγ) production to inhibit tumor growth. However, induction of severe hypertriglyceridemia and fatty liver by T317 limits its application. The naphthylacetic acid modified D-enantiomeric-glycine-phenylalanine-phenylalanine-tyrosine (D-Nap-GFFY) can form a nanofiber hydrogel which is selectively taken up by antigen-presenting cells (APCs). In this study, we determined if D-Nap-GFFY-encapsulated T317 (D-Nap-GFFY-T317) can potently inhibit tumor growth while having no adverse lipogenic effects on the liver. Methods: We prepared D-Nap-GFFY-T317 nanofiber hydrogel and subcutaneously injected it into IFNγ deficient (IFNγ-/-) and wild-type (WT) mice with lung carcinoma, either inoculated LLC1 cells or urethane-induced carcinoma. Mice received oral T317 administration were used for comparison. Effects of treatment on tumor growth, lipogenesis and involved mechanisms were investigated. Results: Compared with T317 oral administration, injection of D-Nap-GFFY-T317 more potently inhibited LLC1 tumor growth in mice. The inhibition was dependent on LXR-activated IFNγ expression in APCs. D-Nap-GFFY-T317 increased M1 while reducing M2 type macrophages in tumors. Associated with activation of IFNγ expression, D-Nap-GFFY-T317 enhanced dendritic cell maturation and infiltration into tumors, increased CD3+/CD8+ cells in tumors, and inhibited tumor angiogenesis. Similarly, D-Nap-GFFY-T317 more potently inhibited growth of urethane-induced lung carcinomas than T317 oral administration. In these two tumor models, T317 oral administration, but not D-Nap-GFFY-T317 injection, activated hepatic lipogenesis and induced fatty liver. Conclusion: Our study demonstrates that D-Nap-GFFY-T317 inhibits lung tumor growth without adverse effects on the liver, indicating the hydrogel-encapsulated LXR ligand might be a novel therapy for tumor treatment.

Nuclear delivery of dual anticancer drug-based nanomedicine constructed by cisplatinum-induced peptide self-assembly.

Nuclear delivery of anticancer drugs, particularly dual complementary anticancer drugs, can significantly improve chemotherapy efficacy. However, successful examples are rare. We reported a novel dual anticancer drug-based nanomedicine with nuclear accumulation properties. The nanomedicine was formed by chelation between a drug peptide amphiphile Rh-GFFYERGD (Rh represents Rhein, 1,8-dihydroxy-3-carboxy anthraquinonea) and cisplatinum (Pt). A single molecule of the drug peptide amphiphile could chelate up to 8 equiv. of cisplatinum in the resulting nanofibers. The nanofibers with a 1 : 4 ratio of Rh-GFFYERGD to cisplatinum demonstrated remarkable cellular uptake, and more significantly, superior nuclear accumulation properties. Additionally, the nanofibers could also bind to the DNA molecule more efficiently than those formed by the drug peptide amphiphile. Thus the nanofibers exhibited excellent anticancer properties both in vitro and in vivo. We envision a significant therapeutic potential of the dual anticancer drug-based nanomedicine with cisplatinum in cancer.

Preorganization Increases the Self-Assembling Ability and Antitumor Efficacy of Peptide Nanomedicine.

Inspired by the biological process of phosphorylation for which different sites of the same protein may have different activities and functions, we utilized phosphatase-based enzyme-instructed self-assembly (EISA) to construct self-assembled nanomedicine from the precursors with different phosphorylated sites. We found that, although the obtained self-assembling molecules after EISA were identical, the changes of EISA catalytic sites could determine the outcome of molecular self-assembly. The precursor with the phosphorylated site in the middle preorganized before EISA, while the ones with other phosphorylated sites could not preorganize before EISA. After EISA, the preorganized precursor then resulted in more stable and ordered assemblies than those of the others, which showed increased cellular uptake and up to 1.7-fold higher efficacy in an antitumor therapeutic compared to those assembled from unorganized precursors.

Enhanced cellular uptake and nuclear accumulation of drug-peptide nanomedicines prepared by enzyme-instructed self-assembly.

Subcellular delivery of nanomedicines has emerged as a promising approach to enhance the therapeutic efficacy of anticancer drugs. Nuclear accumulation of anticancer drugs are essential for its therapeutic efficacy because their targets are generally located within the nucleus. However, strategies for the nuclear accumulation of nanomedicines with anticancer drugs rarely reported. In this study, we reported a promising nanomedicine, comprising a drug-peptide amphiphile, with enhanced cellular uptake and nuclear accumulation capability for cancer therapy. The drug-peptide amphiphile consisted of the peptide ligand PMI (TSFAEYWNLLSP), which was capable of activating the p53 gene by binding with the MDM2 and MDMX located in the cell nucleus. Peptide conformations could be finely tuned by using different strategies including heating-cooling and enzyme-instructed self-assembly (EISA) to trigger molecular self-assembly at different temperatures. Due to the different peptide conformations, the drug-peptide amphiphile self-assembled into nanomedicines with various properties, including stabilities, cellular uptake, and nuclear accumulation. The optimized nanomedicine formed by EISA strategy at a low temperature of 4 °C showed enhanced cellular uptake and nuclear accumulation capability, and thus exhibited superior anticancer ability both in vitro and in vivo. Overall, our study provides a useful strategy for finely tuning the properties and activities of peptide-based supramolecular nanomaterials, which may lead to optimized nanomedicines with enhanced performance.

ß-Galactosidase instructed supramolecular hydrogelation for selective identification and removal of senescent cells.

The identification and removal of senescent cells is very important to improve human health and prolong life. In this study, we introduced a novel strategy of ß-galactosidase (ß-Gal) instructed peptide self-assembly to selectively form nanofibers and hydrogels in senescent cells. We demonstrated that the in situ formed nanofibers could alleviate endothelial cell senescence by reducing p53, p21, and p16INK4a expression levels. We also demonstrated that our strategy could selectively remove senescent endothelial cells by inducing cell apoptosis, with an increase in the BAX/BCL-2 ratio and caspase-3 expression. Our study reports the first example of enzyme-instructed self-assembly (EISA) by a sugar hydrolase, which may lead to the development of supramolecular nanomaterials for the diagnosis and treatment of many diseases, such as cancer, and for other applications, such as wound healing and senescence.

A supramolecular hydrogel for spatial-temporal release of auxin to promote plant root growth.

Short peptide-based hydrogels have attracted extensive research interests in drug delivery because of their responsive properties. So far, most drug molecules have been conjugated with short peptides via an amide bond, restricting the release of the native drug molecules. In this study, we demonstrated the effectiveness of an auxin-based hydrogelator linked by a hydrolysable ester bond. Hydrogel I, formed by the gelator (NAA-G'FFY) linked with an ester bond, was able to release 1-naphthaleneacetic acid (NAA), whereas hydrogel II, formed by the gelator without an ester bond (NAA-GFFY), was not. By mixing NAA-G'FFY with Fmoc-GFFY to form a two-component hydrogel, the spatial and temporal release of NAA was achieved, promoting on-site auxin responses including primary root elongation and lateral root formation in the model plant Arabidopsis thaliana. The strategy of using a hydrolysable ester bond to connect drug molecules and self-assembling peptides could lead to the development of supramolecular hydrogels with more controllable drug release profiles.

Responsive peptide-based supramolecular hydrogels constructed by self-immolative chemistry.

Peptide-based supramolecular hydrogels that are stimuli-responsive under aqueous conditions have many potential biological applications, including drug delivery and sensing. Herein, we reported a series of responsive peptide-based supramolecular hydrogels that respond to glutathione (GSH), nitric oxide (NO) and hydrogen sulfide (H2S), which are biologically important signaling molecules. The responsive hydrogelators were designed by "self-immolative" chemistry and constructed by using self-immolative groups to modify short peptides. The self-immolative capping group could be removed in the presence of a corresponding trigger, thus causing gel-sol phase transitions. The potential of our responsive hydrogels for drug release was also demonstrated in this study. Our study offered several candidates of responsive hydrogels for sensing and drug delivery.

Enzyme-assisted peptide folding, assembly and anti-cancer properties.

The α-helix is the most prevalent conformation in proteins. However, formation of the α-helical conformation remains a challenge for short peptides with less than 5 amino acids. We demonstrated in this study that enzyme-instructed self-assembly (EISA) provides a unique pathway to assist the self-assembly of peptides into the α-helical conformation, while a heating-cooling process leads to a conformation more similar to a ß-sheet. The same peptide with different conformations self-assembled into different nanostructures. The peptide with α-helical conformation self-assembled into stable nanofibers and hydrogels, while the other one assembled into an unstable nanoparticle suspension. The nanofiber solution exhibited better stability against proteinase K digestion and an enhanced cellular uptake compared to the nanoparticle solution. Therefore, the nanomedicine formed by the α-helical peptide showed a better inhibition capacity against cancer cells in vitro and significantly inhibited tumor growth in vivo compared to the one formed by the ß-sheet peptide. Our study demonstrates the unique advantages of EISA to assist peptide folding and self-assembly into biofunctional nanomaterials.

Multi-responsive supramolecular hydrogels for drug delivery.

We reported in this study a versatile method to prepare multi-responsive supramolecular hydrogels for drug delivery application.