3.4 Hydrogen bonding analysis
Hydrogen bonding between a ligand and receptor stabilizes their
interaction [16]. It also shows the specificity, metabolization, and
adsorption of the drug. To further explain the conformational stability,
the total number of hydrogen bonds between each scaffold-receptor was
analyzed (Fig.4). It indicated that the scFv and EGFR DIII complex shows
strong bonding interaction throughout the 50 ns of MD simulations.
Analyzing the reference complex of scFv with the receptor, around 13
hydrogen bonds (Orange) were observed in the complex. At the same time,
13, 5, and 4 residues in Scaf1 (Gray), Scaf2 (Blue), and Scaf3 (Red)
were involved in hydrogen interaction with the receptor. The above
detailed H-bond analysis showed that Scaf1 was bound to the EGFR DIII as
effectively and tightly as the reference molecule scFv.