3.5 Molecular interaction of the top scaffolds with EGFR
The 3D interaction of the top 3 scaffolds and the reference molecules of
the panitumumab and scFv were visualized by PyMOL software [17]. The
docked poses demonstrated that all 6 CDR loops in the panitumumab
structure interacted in 12 hydrogen bonds with EGFR D3. Asp50, Phe91,
Asp92, Lue94 in light chain and Asp33, Tyr35, Tyr55, Asn58, Thr59,
Asp100, and Thr103 in heavy chain are involved in H bonds. Analyzing the
SCFV complex showed that CDR regions H1, H2, L1, L2, and L3 interacted
with EGFR by several residues, among which Tyr35, Asn58, and Asp327 are
in common with the panitumumab complex. Selected scaffolds interacted
with receptor through hydrogen bonds of residues in L3, H3, and H2 CDR
loops in Scaf1, H3, L3 in Scaf2, and L3, H2 in Scaf3 (Fig.5). Analyzing
these three scaffolds indicated that Tyr131, Asn134 in Scaf1, Thr28,
Phe60, Asp61 in Scaf2, and Asn107 are in common with reference
molecules. These scaffolds also form hydrophobics contacts with EGFR
DIII, which are presented in table 4. From the visualization study of
all three scaffolds, we observed that the L3 CDR loop involved H-bonding
interactions similar to the reference molecules. It suggests that this
loop plays an important role in scaffold-receptor hydrogen interaction.
From the findings, it can be seen that Scaf1 mimics the conformation of
the protein-receptor complex with all three CDR loops involved.