In Silico Prediction of Tetrastatin-Derived Peptide Interactions with αvβ3 and α5β1 Integrins

Abstract

Background/Objectives: Tetrastatin, the globular non collagenous (NC1) domain of the α4 chain of collagen IV, was previously demonstrated to inhibit melanoma progression. We identified the minimal active sequence (QKISRCQVCVKYS: QS-13) that reproduced the anti-tumor effects of whole Tetrastatin and demonstrated its anti-angiogenic activity mediated through αvβ3 and α5β1 binding. As QS-13 peptide was not fully soluble in aqueous solution, we designed new peptides with better water solubility. The present work aimed to investigate the interactions of ten QS-13-derived peptides, exhibiting improved hydro-solubility, with αvβ3 and α5β1 integrins. Methods: Using bioinformatics tools such as GROMACS, VMD, and the Autodock4 suite, we investigated the ability of the substituted peptides to bind αvβ3 and α5β1 integrins in silico. Results: We demonstrated in silico that all substituted peptides were able to bind both integrins at the RGD-binding site and determined their theoretical binding energy. Conclusions: The new soluble peptides should be able to compete with natural integrin ligands such as fibronectin, but also FGF1, FGF2, IGF1, and IGF2. Taken together, these findings suggest that the QS-13-derived peptides are reliable anti-angiogenic and anti-tumor agents.

Keywords: MD simulations; collagen; integrins; molecular docking; tetrastatin.

Figure 1

Representativeness of the two predominant conformations of QS-13-derived peptides observed by clustering (3 Å cutoff) in a 100 ns molecular dynamics simulation. (A): Peptides without a disulfide bond between cysteine residues; (B): peptides with a disulfide bond between cysteine residues.

Figure 2

Three-dimensional representation of the predominant conformation of QS-13-derived peptides. The amino acids substituted in the original QS-13 are highlighted in blue spheres. Molecular dynamics simulations were processed using the gromos clustering algorithm for peptides without (A–E) or with a disulfide bond (F–J). (A,F): QS-13-1; (B,G): QS-13-2; (C,H): QS-13-3; (D,I): QS-13-4 (E,J): QS-13-5.

Figure 3

Predominant conformations of peptides derived from QS-13 docked onto the αv (blue surface) β3 (red surface) integrin. The area framed in green on the integrin has been zoomed for better visibility. (A–E): Peptides without disulfide bridge between cysteine residues; (F–J): peptides with a disulfide bridge. (A,F): QS-13-1, (B,G): QS-13-2, (C,H): QS-13-3, (D,I): QS-13-4, (E,J): QS-13-5.

Figure 4

Predominant conformations of peptides derived from QS-13 docked onto the integrin α5 (blue surface) β1 (red surface). The area framed in green on the integrin has been zoomed for better visibility. Figures (A–E) correspond to peptides without disulfide bridges between cysteine residues, while figures (F–J) are associated with peptides featuring a disulfide bridge. (A,F): QS-13-1, (B,G): QS-13-2, (C,H): QS-13-3, (D,I): QS-13-4, (E,J): QS-13-5.

Figure 5

Binding free energy (in kcal/mol) for QS-13-derived peptides. Binding energies for QS-13-derived peptides on the αvβ3 integrin without disulfide bridges between cysteine residues (A), with disulfide bridges between cysteine residues (B), on the α5β1 integrin without disulfide bridges between cysteine residues (C), and with disulfide bridges between cysteine residues (D).