*3.7. Molecular Docking and Dynamics*

The interaction between pancreatic α-amylase and both caffeic acid and p-coumaric acid was performed using Autodock 4.2.6. Molecular docking has been widely utilized to study the critical residues and sites involved in protein–ligand interactions. Our in vitro results demonstrated the mode of binding between α-amylase and polyphenols (caffeic and coumaric acid), and these are further validated by employing docking studies. Figure 6A depicts the three-dimensional structure of α-amylase in cartoon form with caffeic acid shown in the catalytic pocket depicted in balls and stick model. Caffeic acid formed six hydrogen bonds (Trp 59, Gln 63, Arg 195, Arg 195, Asp 197 and Asp 197) and three hydrophobic interactions (Trp 58, Trp 59 and Tyr 62) with α-amylase (Figure 6B, Table 5) showing a binding affinity of −5.09 kcal/mol. In comparison, coumaric acid formed H-bonds with Trp 59, Gln, 63, Arg 195, Aand sp 300 (Table 6) and shared the common hydrophobic residues as of caffeic acid.

**Table 5.** Molecular docking parameters for caffeic acid–pancreatic α- amylase interactions obtained through (PLIP).


**Table 6.** Molecular docking parameters for p-coumaric acid–pancreatic α- amylase interactions obtained through PLIP.


The binding affinity observed for the interaction of coumaric acid to α-amylase was −5.04 kcal/mol. It is apparent that caffeic acid forms six hydrogen bonds as compared to

three hydrogen bonds for coumaric acid, revealing that the binding of caffeic acid binds to α-amylase is more significant, validating our earlier observations.

**Figure 6.** Molecular docking of caffeic acid with pancreatic α-amylase. (**A**) Binding of caffeic acid at the catalytic site of pancreatic α-amylase. (**B**) Amino acid residues and the types of forces in stabilizing the pancreatic α-amylase–caffeic acid complex (Discovery Studio). Similarly, for p-coumaric acid with α-amylase (Panels (**C**,**D**)).
