Fig. 2 | Scientific Reports

Fig. 2

From: Study of caspase-6 activity in aggressive HCT116 cells using methotrexate-encapsulated lactoferrin-conjugated solid lipid nanoparticles via in silico and in vitro approaches

Fig. 2

(a) 2D Interaction Map: Shows binding interactions between MTX and Caspase-6 residues, including hydrophobic contacts with Phe263, Cys264, and Val261; hydrogen bonds with Ser218 and Tyr217; and electrostatic interactions with Arg220, Glu221, and Asp262. These interactions increase binding stability and specificity. (b) 3D Binding Pocket Visualization: Illustrates the placement of MTX within the Caspase-6 binding site, showing how hydrophobic, polar, and electrostatic interactions cooperate to optimize ligand positioning and binding. (c) Root means square deviation of backbone atoms of Caspase-6, BCL-2 and MPP-7 in complex with methotrexate during 50 ns MD simulation. (d) Root mean square deviation of methotrexate in the complex of Caspase-6 (green colour), BCL-2 (orange colour) and MPP-7 (blue colour) complex in the 50 ns MD simulation. (e) 3D interaction map of methotrexate with Caspase-6 B- 2D interaction map of methotrexate. (f) Hydrogen bong interactions between methotrexate and Caspase-6 residues throughout the 50 ns MD simulation. (g) Hydrogen bong interactions between methotrexate and BCL-2 residues throughout the 50 ns MD simulation. (h) Hydrogen bong interactions between methotrexate and MPP-7 residues throughout the 50 ns MD simulation.

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