## 3 Results and Discussion
### Binding Interaction Analysis with PLIP  
#### 3.5.1 Interactions with Estrogen Receptor  
Following docking, the PLIP interface was used to study the interactions. Results for ER-\(\alpha\) with peptides are shown in Figure 2 and Supplementary Information Table S2. As shown in Figure 2a, and Supplementary Information Table S2a, Pep exhibited eighteen hydrogen bonds and eight hydrophobic interactions with ER-\(\alpha\). Additionally, a \(\pi\)-stacking interaction between Tyr537A and Tyr6 of Pep, as well as salt bridges between His516D and Lys520D and the carboxy-terminal of Pep, were observed. Tyr537 is a critical residue in the binding pocket of ER-\(\alpha\) that plays an important role in hormone binding and DNA binding and is essential for the conformational changes that occur within the receptor to \begin{table}
\begin{tabular}{c c c c c c} \hline \hline  & \multicolumn{5}{c}{**ER-\(\alpha\)**} \\ \hline
**Petide Sequence** & **Carnosic Acid** & **Chlorogenic Acid** & **Gallic Acid** & **Rosmarianic Acid** &
\begin{tabular}{c} **Neat Peptide** \\ **(Unconjugated)** \\ \end{tabular} \\ \hline YHWYGYITQN (pep) & \(-8.7\) & \(-9.8\) & \(-8.8\) & \(-10.3\) & \(-10.0\) \\ \hline FHWYGYITQN (Mut1) & \(-7.8\) & \(-10.2\) & \(-9.0\) & \(-8.7\) & \(-8.6\) \\ \hline YHWYGYITQN (Mut2) & \(-7.8\) & \(-9.6\) & \(-9.5\) & \(-8.6\) & \(-8.6\) \\ \hline YHWYGYITQN (Mut3) & \(-10.0\) & \(-9.1\) & \(-8.1\) & \(-8.2\) & \(-10.0\) \\ \hline YHWYGYITQD (Mut4) & \(-9.0\) & \(-10.3\) & \(-10.2\) & \(-9.4\) & \(-9.1\) \\ \hline \multicolumn{5}{c}{**PPAR-\(\alpha\)**} \\ \hline
**Petide Sequence** & **Carnosic Acid** & **Chlorogenic Acid** & **Gallic Acid** & **Rosmarianic Acid** &
\begin{tabular}{c} **Neat Peptide** \\ **(Unconjugated)** \\ \end{tabular} \\ \hline YHWYGYITQN (pep) & \(-7.1\) & \(-8.1\) & \(-8.3\) & \(-9.2\) & \(-8.9\) \\ \hline FHWYGYITQN (Mut1) & \(-6.5\) & \(-7.0\) & \(-8.3\) & \(-9.5\) & \(-9.1\) \\ \hline YHWYGYITQN (Mut2) & \(-6.2\) & \(-7.1\) & \(-9.2\) & \(-5.4\) & \(-7.6\) \\ \hline YHWYGYITQN (Mut3) & \(-6.5\) & \(-7.2\) & \(-7.4\) & \(-7.6\) & \(-8.9\) \\ \hline YHWYGYITQD (Mut4) & \(-7.0\) & \(-6.8\) & \(-8.6\) & \(-8.3\) & \(-9.1\) \\ \hline \multicolumn{5}{c}{**EGFR**} \\ \hline
**Petide Sequence** & **Carnosic Acid** & **Chlorogenic Acid** & **Gallic Acid** & **Rosmarianic Acid** &
\begin{tabular}{c} **Neat Peptide** \\ **(Unconjugated)** \\ \end{tabular} \\ \hline YHWYGYITQN (pep) & \(-8\) & \(-8.5\) & \(-8.3\) & \(-8.4\) & \(-9.5\) \\ \hline FHWYGYITQN (Mut1) & \(-8.3\) & \(-8.3\) & \(-7.7\) & \(-9.1\) & \(-7.7\) \\ \hline YHWYGYITQN (Mut2) & \(-7.2\) & \(-8.2\) & \(-7.7\) & \(-8.4\) & \(-8.7\) \\ \hline YHWYGYITQN (Mut3) & \(-8.6\) & \(-7.4\) & \(-7.4\) & \(-7.4\) & \(-8.0\) \\ \hline YHWYGYITQD (Mut4) & \(-8.1\) & \(-7.5\) & \(-8.4\) & \(-8.8\) & \(-8.3\) \\ \hline \hline \end{tabular}
\end{table} 
Table 4: Binding Affinities (kcal/mol) of Peptide, mutants and Peptide-Polyphenyl Conjugates for ER-\(\alpha\); PPAR-\(\alpha\), and EGFR using Autodock Vina. activate downstream transcription processes [57]. This indicates that Pep interacts within the same region. For the Mutation 1 peptide (Mut1), which involved altering the N-terminal Tyr to Phe, results are shown in Figure 2b and Supplementary Information Table S2b. Fifteen H-bonds and eleven hydrophobic interactions were observed; an H-bond with Asp426 that had been observed for the original peptide was eliminated, which explains the reduction in binding affinity upon mutating Y to F. No \(\pi\)-stacking or salt bridges occurred, due to a slight change in orientation of the ligand within the receptor binding site. The mutation of His to Ile (Mut2) resulted in fourteen H-bonds and five hydrophobic interactions with ER-\(\alpha\), as seen in Figure 2c and Supplementary Information Table S2c. Interestingly, with the exception of one H-bond with Asp426D, H-bonds with different residues of ER-\(\alpha\) were formed compared to those with Pep.