## 3 Results and Discussion
### Molecular Dynamics Studies
#### 3.6.2 Protein-Ligand Interactions
For Mut2 (Figure 11c), Thr 279 and Glu 282 also showed significant H-bonding. The total P-L contacts showed a gradual increase from 15 to 20 throughout the simulation. For Mut3 (Figure 11d), similar residues showed H-bonding, but Mut3 appeared to have the lowest number of P-L contacts of all the peptides. The total P-L contacts showed a gradual decrease from 18 to 12 throughout the simulation. For Mut4 (Figure 11e), Tyr334 showed significantly less H-bonding and hydrophobic interactions, indicating that the Tyr334 residue was less able to interact with the receptor due to the mutations of Mut4. The total protein-ligand contacts fluctuated around 18 for the simulation. In previous studies, Thr279 has been implicated in binding of ligands to PPAR-\(\alpha\)[73], as has Tyr334. This indicates that that some of the conjugates also interact in the same region. The interactions showing the ligand-atom contacts for each of the peptide ligands with PPAR-\(\alpha\) are shown in Supplementary Information Figure S10. Figure 11: Protein ligand contacts of PPAR\(\alpha\)-ligand complexes with (**a**) Pep (top); total number of contacts with Pep (bottom); (**b**) Mut1 (top); total number of contacts with Mut1 (bottom); (**c**) Mut2 (top); total number of contacts with Mut2 (bottom); (**d**) Mut3 (top); total number of contacts with Mut3 (bottom); (**e**) Mut4 (top); total number of contacts with Mut4 (bottom). For the polyphenol-peptide conjugates, results for the protein-ligand contacts obtained are shown in Figure 12. For RMAPep (Figure 12a), Glu286 played a major role in H-bonding followed by Tyr334, which was also implicated in hydrophobic interactions in addition to several other residues. The total P-L contacts increased in the first 30 ns of the simulation and then steadily fluctuated around 20 contacts. For RMAMut1 (Figure 12b), Glu282 played a major role in both H-bonding and water bridges in addition to Tyr 334, His 457 and Lys 257 which also showed hydrophobic interactions. The total protein-ligand contacts fluctuated around 18 for the first 60 ns and then dropped to around 15 for the remainder of the simulation. For GLAMut1 (Figure 12c), Tyr334 showed the highest interaction fraction involved in H-bonding, hydrophobic interactions, and water bridges. The total protein-ligand contacts varied throughout the simulation, showing an overall decrease to about 18 contacts by the end of the simulation. For GLAMut2 (Figure 12d), more H-bonding was seen than any other conjugate, with Glu286 playing the largest role in H-bonding. The total protein-ligand contacts remained very steady throughout the simulation, fluctuating around 18 contacts. For CGAMut4 (Figure 12e), Glu282 played a large role in water bridges, but many residues seemed to play an important role in interacting with the receptor. The total protein-ligand contacts showed a gradual increase throughout the simulation, ending with about 24 contacts. Finally, for CSAMut4 (Figure 12f), Arg226 played a major role in H-bonding, hydrophobic interactions, and water bridges. The total protein-ligand contacts showed an initial drop from about 10 to 5 contacts in the first 5 ns of the simulation, followed by a slight increase to about 7 contacts by the end of the simulation. Overall, the different polyphenol-peptide conjugates showed very different protein-ligand contacts with highest interactions being observed for CGAMut4; RMAMut1 and GLAMut1. Tyr 334 interactions were found to be common in all cases, indicating a combination of hydrophobic and H-bonding interactions which stabilized these complexes. The individual ligand-atom interactions for each of these complexes are shown in Supplementary Information Figure S11, which corroborates with the histogram results obtained for the Protein-Ligand contacts. Overall, for all polyphenol-peptide conjugates, H-bonding interactions, hydrophobic interactions and water-bridges played a major role in binding interactions. Figure 12: Protein ligand contacts of PPAR\(\alpha\)-ligand complexes.