## 3 Results and Discussion
### Molecular Dynamics Studies
#### 3.6.1 Analysis of RMSDs and RMSFs for Ligand-Receptor Complexes
Mut3 seems to gradually migrate up the binding pocket throughout the 100 ns while also increasing in compactness by slightly folding in on itself. All peptides are shown to remain fully attached to the PPAR-\(\alpha\) receptor for the entire simulation, while Mut1 appears the least strongly bound and Mut2 appears the most tightly attached. We then examined the trajectories of the polyphenol-peptide conjugates with PPAR-\(\alpha\) (Supplementary Information Figure S5). Like the peptides, most of the polyphenol-peptide conjugates appear to initially bind within the binding pocket of the PPAR-\(\alpha\) receptor (except CSAMut4 and CGAMut4). RMAPep appears the most compact within the receptor compared to all other compounds. GLAMut1 shows more movement within the receptor binding pocket, especially in the first 25 ns, and it remains mostly unfolded throughout the simulation. Furthermore, it appears to move away from the helical region into the loop region after 50 ns. RMAMut1 also shows a slight initial change in position followed by high stability within the binding pocket and keeps a relatively less compact, more open conformation. GLAMut2 also shows a slight initial change in position followed by high stability within the binding pocket with a relatively less compact conformation. The binding for GLAMut1, RMAMut1, and GLAMut2 look very similar in terms of ligand position within the binding pocket and ligand compactness. CGAMut4 and CSAMut4 are relatively loosely attached to the PPAR-\(\alpha\) binding pocket and are attached on the peripheral alpha helical regions and loops. Additionally, the ligands remain partly outside of the binding pocket. However, CGAMut4 remains in the same position for the entirety of the simulation whereas CSAMut4 shows significant movement. CGAMut4 and CSAMut4 also show binding on opposite sides of the PPAR-\(\alpha\) receptor. Based on the trajectory images, CSAMut4 appears the least attached and least stable while RMAPep appears to remain the most well attached to the receptor. The EGFR model structure selected is that of the EGFR kinase domain, which has a bilobate structure, with the N-terminal group consisting of mostly beta-strands and one alpha-helix while the C-terminal lobe constitutes of primarily \(\alpha\)-helical structures. The cleft to which several ligands and ATP analogues are found to bind is found between the two lobes [70]. The catalytic domain is surrounded by the cleft and consists of the glycine-rich nucleotide phosphate-binding loop (Gly695-Gly700), while the C-lobe contributes the DFG motif (Asp831-Gly833), the catalytic loop (Arg812-Asn818), and the A-loop (Asp831-Val852) [71]. The RMSF graphs for EGFR are shown in Figure 8h,i corresponding to the peptide-bound receptor and the polyphenol-peptide bound receptor, respectively. For the peptide-bound receptors, major fluctuations are observed with Lys867 along with Ser921, Lys929 and Met987 with the highest fluctuations being seen for Mut1 and Pep. For the conjugates, fluctuations were observed at the same residues as the peptide, along with those seen at Ala722, Val738, Arg748 and Ser784. The later residues showed less intense fluctuations comparatively, though the values were higher for the conjugates compared to the unconjugated peptides. In previous work, it has been observed that the residues located in the loop or helix parts of receptors show higher RMSF fluctuations particularly in the \(N\)- and \(C\)-terminal regions [72]. The same was also observed in the case of the peptides and the polyphenol conjugate interactions with EGFR. To further probe these results, we analyzed the corresponding trajectories (Supplementary Information Figure S6). Pep appears to bind to the hinge region. For the first 50 ns of the simulation, the ligand appears to undergo conformation changes within the cleft; however, after 75 ns, minimal changes were observed, indicating that the ligand was tightly bound to the pocket by the end of the simulation.