Diketopiperazines (DKPs) have emerged as promising candidates for treating diverse diseases, particularly cancer. In this context, 2,5-diketopiperazines have been extensively investigated in comparison with 2,6-diketopiperazines. This work explores the selectivity and impact of 2,6-diketopiperazine enantiomers derived from alpha-amino acids on MDA-MB-231 triple-negative breast cancer cells (TNBC). This subtype of cancer is recognized for its aggressiveness and the lack of effective therapeutic options. The evaluation utilized MTT and flow cytometry assays to examine the impact of 2,6-DPKs on the MDA-MB-231 breast cancer cell line. The obtained IC50 values for compounds 1 and (S)-enantiomers ranged from 4.6 mu M to 4.944 mM, where 1 and (S)-2a exhibited the lowest values. The IC50 values for (R) enantiomers ranged from 0.021 to 3.639 mM, whereas (R)-2b was the lowest. Flow cytometry results revealed that compounds increase in apoptosis at 48 h compared to 24 h, ranging from 54.1% to 76.2%; however, (S)-12a exhibited a 3% decrease in apoptotic induction at 48 h. All investigated 2,6-diketopiperazines derived from alpha-amino acids showed potential as anticancer agents against MDA-MB-231 cancer cells. In particular, compounds 1, (S)-2a, -4a, and -5a showed remarkable inhibitory effects on proliferation, viability, and apoptosis. The MTT results in the culture of healthy cells of the kidney line Vero did not display cytotoxicity at the tested concentrations up to 12.0 mM. Hence, these 2,6-DPKs are suitable for in vivo testing shortly.