## 3 Results and Discussion
### Binding Interaction Analysis with PLIP
#### 3.5.2 Interactions with PPAR-\(\alpha\)  
Peroxisome proliferatorator-activated receptors (PPARs) are members of the nuclear hormone receptor superfamily that are responsible for cellular responses. PPARs are regulators of lipid and carbohydrate metabolism; they also modulate inflammatory responses [60]. Their over-expression has also been implicated in breast cancer. PPARs are activated by a variety of ligands, including cholesterol metabolites, eicosanoids, retinoids, fatty acids, steroids and several antidyslipidemic drugs [61]. In previous studies, the crystal structure of the PPAR-\(\alpha\) ligand binding domain (LBD) in complex with a polyphenic dihydro cinnamate derivative was studied; it was shown that a conserved H-bonding network formed between the cinnamate derivative and the AF2 helix played an important role in forming a stable structure. This study further showed that the LBD of PPAR-\(\alpha\) occurred at the C-terminus, composed of 12 helices in an antiparallel helix sandwich, as well as a 3-stranded antiparallel \(\beta\)-sheet. Ligands generally bind to Tyr437, Tyr446, Ser280, and His440 of the PPAR-\(\alpha\) ligand-binding motif [62]. In another study, molecular docking of several benzenesulfphinamide derivatives with PPAR-\(\alpha\) revealed residues including Met355, Met330, Met220, Val332, Val334, Ile331, Leu331, Leu321, Ser280, Asn219, Gly335, and Cys276, among others, that were involved in interactions [63]. The PLIP results showing the residues of the PPAR-\(\alpha\) receptor involved in binding interactions with the peptides are shown in Figure 4 and Supplementary Information Table S4. The binding interactions for Pep with PPAR-\(\alpha\) showed ten hydrophobic interactions and twelve hydrogen bonds, shown in Figure 4a and Supplementary Information Table S4a. Met220A, Ile241A, Val281A, Leu321A, and Val332A were involved in hydrophobic interactions and Ala256A, His274A, Leu331A, Gly335A, Ala455A, and His457A were involved in H-bonding, while Lys257A, Thr279A, Ala333A, and Tyr334A were involved in both hydrophobic interactions and H-bonding. For Mut1 (Figure 4b and Supplementary Information Table S4b), thirteen hydrophobic interactions, twelve H-bonds, and a \(\pi\)-stacking interaction with Tyr334A were observed. New hydrophobic interactions were observed with Thr283A, Met320A, and Val324A, while new H-bonds occurred with Leu254A, Thr283A, and Thr285A. For Mut2, extensive hydrogen bonding (fourteen) and hydrophobic interactions (eleven) were observed compared with Pep, and a \(\pi\)-stacking interaction with Tyr334A was again observed, as shown in Figure 4c and Supplementary Information Table S4c. New hydrogen bonds occurred with Tyr214A, Lys222A, Leu254A, and Ser323A, while new hydrophobic interactions were seen with Glu282A, and Met320A. Mut3 (Figure 4d and Supplementary Information Table S4d) exhibited thirteen hydrophobic interactions and sixteen H-bonds. New hydrophobic interactions occurred with Val255A, Thr283A, Thr285A, Glu286A, Glu289A, and Val324A, while new H-bonds occurred with Asn217A, Asn219A, Met220A, Glu282A, Thr283A, Glu286A, and Glu289A. Mut4 (Figure 4e and Supplementary Information Table S4e), displayed ten hydrophobic interactions and ten hydrogen bonds. New hydrophobic interactions were observed with Lys224A, Asn236A, Leu254A, and Val324A and new H-bonds were seen with Lys224A, Ser234A, Thr253A, and Thr283A. A salt bridge was formed with Lys224A. PLIP interactions of the peptide-polyphenylenol conjugates and PPAR\(\alpha\) were next examined as shown in Figure 5 and Supplementary Information Table S5. The CGAPep conjugate displayed seventeen H-bonds and fourteen hydrophobic interactions as well as two \(\pi\)-stacking interactions (Figure 5a and Supplementary Information Table S5a). New hydrogen bonds formed included those with Lys216A, Asn219A, Leu254A, Cys278A, Thr279A, Glu282A, Thr285A, and Glu696B, while new hydrophobic interactions were seen with Val255A, Leu258A, Glu282A, Ile339A, and Leu693B compared to Pep.