Development of the Antithrombotic Peptide LEKNSTY Targeting the Collagen Surface: II. Improvement of Plasma Stability

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...