In silico molecular docking analysis of chlorotoxin-derived peptide interaction with MMP-2

Abstract

Objectives: This study aimed to investigate the interaction between chlorotoxin (CTX) and matrix metalloproteinase-2 (MMP-2) using in silico molecular docking.

Materials and methods: The three-dimensional structures of human MMP-2 (PDB ID: 1CK7) and CTX (PDB ID: 1CHL) were retrieved from the Protein Data Bank and prepared for docking analysis. Molecular docking was performed with AutoDock Vina version 1.2, focusing on the catalytic region of MMP-2. The resulting docking poses were analyzed for predicted binding affinity, spatial orientation, and residue-level interactions.

Results: Docking analysis identified several energetically favorable CTX binding poses on the MMP-2 surface. The top-ranked pose had a predicted binding affinity of –9.1 kcal/mol, with additional conformations showing affinities of –8.5, –8.2, and –7.9 kcal/mol. The most favorable binding mode was localized near the catalytic region of MMP-2, including residues adjacent to the zinc-binding pocket, but it did not clearly occupy the catalytic center. Key putative interactions involved Glu404, Asp410, His403, Glu412, Leu399, and Val400, suggesting stabilization through hydrogen bonding, electrostatic interactions, and hydrophobic contacts.

Conclusion: The present findings support the structural feasibility of CTX association with MMP-2 and suggest a surface-associated binding mode near the catalytic region rather than a classical deep active-site inhibitory interaction. These results provide a useful structural framework for future biochemical and cellular studies aimed at clarifying the role of CTX-MMP-2 recognition in glioma-associated systems.

Cite this article as: Demirezen A. In silico molecular docking analysis of chlorotoxin-derived peptide interaction with MMP-2. D J Med Sci 2026;12(1):36-43. doi: 10.5606/ fng.btd.2026.215.