Exploration of type II and III collagen binding interactions with short peptide-phenyl pyrazole conjugates via docking, molecular dynamics and laboratory experiments

Abstract

ABSTRACT Interaction with components of the extracellular matrix, particularly various forms of collagen, is essential for the design of successful scaffolds for tissue engineering applications. Both Type II and Type III collagen are found in various connective tissues in the body, providing stability, wound healing, and in some cases assisting in fibrillogenesis. In this study, we designed short peptide conjugates with phenyl pyrazole moieties and examined their interactions with Type II and III triple helical collagen models. The number of hydrophobic groups was varied by varying the phenyl pyrazole moieties that were conjugated with three separate peptides (SYED; SLKD and SLYD). Molecular dynamics (MD) and docking studies revealed that in most cases conjugating with phenyl pyrazole improved binding affinity and stability compared to neat peptides. Computational studies were also carried out to examine the formation of stable scaffold assemblies using MD simulations by integrating the peptide conjugates with either Type II or III collagen and chondroitin sulfate, in order to mimic the formation of a scaffold. As a proof of concept, we examined the binding interactions of the short peptides with Type II and III collagen using SPR and CD spectroscopy, and then synthesized two of the peptide conjugates and integrated them with either Type II or Type III collagen and chondroitin sulfate by layer-by-layer assembly to develop scaffolds to validate computational results. AFM imaging showed the formation of fibrillary structures. The cytocompatibility of the scaffolds was then examined in the presence of mesenchymal stem cells, that showed the formation of cell-scaffold matrices particularly with SLYD conjugates. Our results indicate that such peptide-pyrazole conjugates, may be developed for designing scaffolds for tissue engineering applications.