Background: Cardiovascular diseases (CVDs) represent the most prevalent non-communicable diseases worldwide. In 2019, around 17.9 million individuals succumbed to cardiovascular diseases, accounting for 32% of all global fatalities. Mitochondria are essential for maintaining cellular metabolic equilibrium, facilitating cell survival and apoptosis, and generating the majority of cellular energy. Protein–protein interactions (PPIs) play a crucial role in both physiological and pathological processes, with abnormal PPIs linked to numerous disorders, making them prospective pharmacological targets across diverse therapeutic domains. Peptides are highly promising as protein-protein interaction inhibitors due to their capacity to replicate natural interaction patterns and encompass rather extensive interaction regions. Computational methods are extensively employed to accelerate drug discovery by screening prospective lead molecules. Purpose: Current work was designed to check efficacy of Daucus carota flavonoid for cardioprotective activity. Methodology: Scientific validation of the current investigation was done by computational based molecular docking study of lead molecules of Daucus carota pulp against malonyl Co-A decarboxylase enzyme. Result: The flavonoid found in D.carota has been identified as an effective cardioprotective drug and their lead molecules luteolin and apigenin demonstrating effective binding to the target protein malonyl Co-A decarboxylase with binding energies of -7.34 and -7.12 kcal/mol, respectively. Conclusion: The findings indicated that each selected lead chemical for additional investigation shown significant inhibitory activity against malonyl Co-A decarboxylase, hence revealing its cardio protection potential.