Fig. 5

Molecular docking and Molecular dynamics result analysis. A. The probable binding conformations of TDCPP-MMP3 are shown. B. The binding of TDCPP to surrounding amino acids is illustrated. C. The binding energy of TDCPP with MMP3 is presented. D. RMSD plot comparing the structural dynamics of the protein-only system (blue trace) and the TDCPP-MMP3 protein-ligand complex (red trace) throughout the molecular dynamics simulation. E. RMSF plot illustrating the residue-specific flexibility profiles of the TDCPP-MMP3 complex. F. Rg plot demonstrating the compactness evolution of the TDCPP-MMP3 complex during the simulation. G. SASA plot depicting the temporal changes in surface exposure of the protein-ligand complex, reflecting conformational adjustments and solvent interactions. H. H-bond count plot quantifying the number of intermolecular hydrogen bonds formed between the TDCPP ligand and MMP3 protein residues during the molecular dynamic trajectory.