Development of the Antithrombotic Peptide LEKNSTY Targeting the Collagen Surface: I. Design and Validation

Production of bioactive peptides by high-voltage pulsed electric field: Protein extraction, mechanism, research status and collaborative application

Bioactive peptides exhibit a variety of potential applications in the fields of medicine, food and cosmetics. However, studies have shown that the traditional preparation is characterized by low efficiency, substantial pollution, limited activities and poor purity, which constrains their further application. High-voltage pulsed electric field (HPEF) technology, as a physical non-thermal processing method, shows unique advantages in bioactive peptide preparation. Through comprehensive analysis, this paper reveals the main principle of HPEF technology, the extraction of proteins (break up cellular tissue), the structural changes of proteins, enzymes and bioactive peptides after treatment, the improvement of bioactive peptides' functional properties and the potential in promoting bioactive peptides' large-scale production. Besides, this paper introduces the application of other non-thermal processing technologies, artificial intelligence and nanotechnology, providing new ways of thinking for the efficient preparation and application of bioactive peptides and establishes a theoretical foundation for the application and promotion of HPEF technology.

Network pharmacology and transcriptomics reveal androgen receptor as a potential protein target for 6PPD-quinone

N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine quinone (6PPD-quinone, or 6PPD-Q) has received increasing attention as an emerging hotspot contaminant. The occurrence of 6PPD-Q in dust and fine atmospheric particles indicates substantial human exposure to this toxicant but the hazards of 6PPD-Q to human health is unknown. We used in silico approaches to identify potential human protein targets of 6PPD-Q and conducted preliminary validation through an in vitro cell proliferation assay and an in vivo transcriptomic analysis of prostate tissues from 6PPD-Q-treated mice. Receptor-based reverse screening and network pharmacology identified four hub targets of 6PPD-Q that were closely related to prostate carcinogenesis. Among these four targets, 6PPD-Q exhibited a strong binding tendency to androgen receptor (AR) with a binding free energy of -23.04 kcal/mol. A support vector machine (SVM) model for predicting chemicals with AR agonism or AR-inactivity was established with good prediction performance (mean prediction accuracy: 0.92). SVM prediction and AR-mediated cell-based assays, with a known AR agonist and a proposed AR inactive agent as positive and negative controls, confirmed that 6PPD-Q displayed AR agonism. Upregulation of Ar mRNA expression (FC = 1.29, p = 0.0404) and its related prostate cancer pathway was observed in the prostate of mice exposed to environmentally realistic concentrations of 6PPD-Q, suggesting a potential role in promoting prostate carcinogenesis. These findings provide evidence that 6PPD-Q agonized AR to exert downstream gene transactivation and imply its prostate cancer risks to humans.

Intelligent Design of Antithrombotic Peptide Targeting Collagen

Binding of blood components to collagen was proved to be a key step in thrombus formation. Intelligent Design of Protein Matcher (IDProMat), a neural network model, was then developed based on the principle of seq2seq to design an antithrombotic peptide targeting collagen. The encoding and decoding of peptide sequence data and the interaction patterns of peptide chains at the interface were studied, and then, IDProMat was applied to the design of peptides to cover collagen. The 99.3% decrease in seq2seq loss and 58.3% decrease in MLP loss demonstrated that IDProMat learned the interaction patterns between residues at the binding interface. An efficient peptide, LRWNSYY, was then designed using this model. Validations on its binding on collagen and its inhibition of platelet adhesion were obtained using docking, MD simulations, and experimental approaches.

Biomimetic Design of Peptide Inhibitor to Block CD47/SIRPα Interactions

CD47 on the surface of tumor cells has become a research hot spot in immunotherapy and anticancer therapy, as it can bind to SIRPα protein on the surface of macrophages, which ultimately leads to immune escape of tumor cells. In the present study, molecular interactions between CD47 and human SIRPα proteins (including variant 1, V1 and variant 2, V2) were analyzed through molecular dynamics (MD) simulation and the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method. Hydrophobic interactions were found as the main driving force for the binding of CD47 on SIRPα. The residues including pyroglutamate acid (Z)1, L2, E35, Y37, E97, L101, and T102 of CD47 were identified with a significant favorable contribution to the binding of CD47 on SIRPα (both V1 and V2). Based on this, a peptide inhibitor library with the sequence ZLXRTLXEXY was designed (X represents the arbitrary residue of 20 standard amino acids) and then screened using molecular docking, MD simulations, and experimental validation. Finally, a peptide ZLIRTLHEWY was determined with high affinity with SIRPα from 8000 candidates, containing 6/10 residues favorable for the binding on SIRPα V1 and 8/10 residues favorable for the binding on SIRPα V2, which was thus considered to have potential anticancer function.

Design and characterization of antithrombotic ClEKnsTy-Au nanoparticles as diagnostic and therapeutic reagents

Thrombosis can cause various cardiovascular diseases, which seriously endanger human life. Development of diagnostic and therapeutic reagents for thrombosis at an early stage would be helpful for the improvement of treatment and the reduction of mortality. In the present study, based on an antithrombotic peptide lEKnsTy (lowercase letters represent D-amino acid residues), a diagnostic and therapeutic reagent targeting collagen and the early stage of thrombosis was proposed, where cysteine was introduced into the amino terminus of lEKnsTy to prepare ClEKnsTy, followed by coupling with AuNPs to prepare nanoconjugate AuNP-Cl. The binding of AuNP-Cl on the collagen surface was then confirmed by the molecular dynamics simulations of the binding of ClEKnsTy on collagen, and the experimental results of the binding of AuNP-Cl on collagen. The inhibition of platelet adhesion on the collagen surface by AuNP-Cl was also confirmed. Moreover, the good imaging ability of AuNP-Cl was confirmed by dark-field microscopy. These results indicated that AuNP-Cl was a potential effective diagnostic and therapeutic reagent targeting collagen, which would be helpful for the research and development of multifunctional antithrombotic reagents.

Development of antithrombotic peptides based on the molecular interactions between von Willebrand factor and GPIbα

Binding of platelets on vascular endothelia at the damaged site using von Willebrand factor (vWF) as a bridge is of great significance for platelet adhesion and subsequent arterial thrombosis. Molecular...