Molecular docking studies were conducted to further elucidate the phenolic compounds that might be responsible for the increased expression of UCP1 and PPARα in CPEF-treated db/db mice. Seven of the eight major phenolic polyphenols identified in CPEF were used for the molecular docking procedure. The flavanone, eriodictyol-
O-deoxyhexose-
O-hexose, was excluded due to the unknown position and the identities of the sugar moieties in the molecular structure. The 2-D structures of the compounds were then drawn using ChemDraw (Version 8.0, PerkinElmer Informatics, Waltham, MA, USA) and optimised using Avogadro (Version 1.2) [62 (
link)], in which partial charges were added using the Ghemical force field, followed by energy minimisation to obtain the optimal geometry for each compound.
The 3-D models of
Mus-musculus UCP1 and PPARα were modelled using the Swiss-Model online tool [63 (
link)]. Both UCP1 and PPARα were homology modelled for this study due to the lack of
Mus-musculus crystal structures. The template used to generate the UCP1 model was PDB ID 2LCK, whilst the templates used for the PPARα model were PDB ID’s 3DZY and 1K7L. Models were validated using the MolProbity online server [64 (
link)]. Using UCSF Chimera (Version 1.15) [65 (
link)], the protein structures were optimised for molecular docking by removing the water molecules and all non-standard residues. The molecular docking simulation was then carried out using Autodock Vina software Version 1.2.0 [66 (
link)], with the docking grid box co-ordinates presented in
Table 2. Based on the Autodock Vina scoring technique, the docked complexes were ranked on binding affinity score and the root mean square deviation from the original structural pose of each compound. All complexes were superimposed to ensure the validation of the docking procedure and binding site (
Figure S1). Following the molecular docking procedure, the predicted intermolecular interactions, stabilising the compound within the active site of each protein, were assessed using the ligplot application of the Ligplus software Version 2.2 [67 (
link)]. The intermolecular interactions identified in each docked complex, comprising hydrophobic interactions and hydrogen bonds, were analysed and compared to CL-316,243 and fenofibrate (experimental control standards), which are compounds previously reported to experimentally activate UCP1 and PPARα expression, respectively [53 (
link),54 (
link)].
Jack B.U., Ramharack P., Malherbe C., Gabuza K., Joubert E, & Pheiffer C. (2023). Cyclopia intermedia (Honeybush) Induces Uncoupling Protein 1 and Peroxisome Proliferator-Activated Receptor Alpha Expression in Obese Diabetic Female db/db Mice. International Journal of Molecular Sciences, 24(4), 3868.