Monascus sp. produces biopigments (ankaflavin, monascin, and rubropunctatin) that have various biological activities, including a role in lipid metabolism through interaction with peroxisome proliferator-activated receptor alpha (PPAR-α). It plays an important role in regulating lipid metabolism and is a therapeutic target. Fenofibrate is one of the antihyperlipidemic drugs that targets PPAR-α. Therefore, this study aimed to evaluate the interaction of ankaflavin, monascin, and rubropunctatin with PPAR-α. The biopigments were analyzed using SwissADME and molecular docking with PPAR-α (PDB ID: 5HYK). The results showed that ankaflavin, monascin, and rubropunctatin complied with Lipinski’s Rule. Molecular docking revealed that all biopigments analyzed had good interactions with PPARα, with binding affinity values of ankaflavin -10.03 kcal/mol, monascin -10.38 kcal/mol, and rubropunctatin -10.62 kcal/mol. Rubropunctatin had the most negative binding affinity and the lowest predicted Ki (16.45 µM) among the tested biopigments and was most similar to the positive control, fenofibrate (−10.78 kcal/mol and 12.59 µM). In conclusion, these findings suggest that biopigments from Monascus sp. are potential candidates for PPAR-α modulators, particularly rubropunctatin. Further in vivo and in vitro investigations are necessary to validate these findings.
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