The peroxisome proliferator-activated receptors (PPARs) are important molecular targets for the development of drugs for the treatment of human metabolic diseases, inflammation, and cancer. They are known to be activated by a variety of structurally diverse compounds. Using a structure-based drug design approach, we designed and synthesized a series of novel isoxazolyl-serine-based PPAR ligands possessing moderate affinities. Some of the new PPAR ligands were able to stimulate cardiomyocyte differentiation from murine ES cells. Ligand 1a was the most active one tested at concentrations between 1.25 to 20 muM between days 2-6, coinciding with the period when mesodermal cells can be recruited to become cardiomyocytes. Notably, the known PPARalpha, gamma, and delta agonists tested, e.g., fenofibrate, rosiglitazone, and GW501516, were inactive in this assay.