Theobroma cacao provides precious products such as polyphenol-rich beans that are useful for nutraceutical purposes. The geographical area may influence the chemical composition of raw cocoa beans in terms of the polyphenols and biological qualities of the products. This work aimed to investigate the biological properties and the chemical composition of two different samples of Criollo var. cocoa raw beans coming from two areas (Indonesia; Peru). Beans underwent biphasic extraction obtaining lipophilic and hydroalcoholic extracts. The extracts were tested for antiradical, antimutagenic, and antigenotoxic effects. Cell viability inhibition toward breast, gastric/esophageal colorectal adenocarcinoma, and hepatoblastoma human cell lines was evaluated. Extracts were chemically investigated through UV-Vis spectroscopy and ultra-high-pressure liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QqTOF MS/MS). Results showed that the Indonesian bean hydroalcoholic extracts were able to scavenge 2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) cation radical better than the Peruvian hydroalcoholic extracts (ECs50: 72.63 vs. 322.20 μg/mL). Extracts showed antimutagenic and antigenotoxic activity. The viability inhibitory effect on breast and hepatic cancer cells was reached only for the Indonesian hydroalcoholic extracts at hundreds of μg/mL. Phenylpropenoyl-L-amino acids, hydroxycinnamoyl aminoacids conjugates, and procyanidin compounds were found mainly in the hydroalcoholic extracts, whereas fatty acids and lyso-phospholipids were found mainly in lipophilic fractions. Fatty acid and (epi)catechins appeared to be affected by different environmental conditions of the geographical areas.
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