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Cynomorium plants contain large amount of flavonoids with flavan-3-ols being the major ones. Other sub-flavonoid
types in Cynomorium plants are flavones, flavonols, and flavanones. From the aqueous extract of the stems of C. songaricum,
catechin, procyanidin B-1 , procyanidin B-6 , flavan-3-ol trimers, flavan-3-ol tetramers, flavan-3-ol pentamers, and flavan-3-ol polymers (condensed tannins) were obtained. Thiolytic degradation of the flavan-3-ol polymers yielded benzylthioepicatechin, indicating that the extender flavan unit of the condensed tannin is mainly epicatechin . The flavan-3-ol polymers showed inhibitory activity against HIV PR with the activity increased as the molecular weight increased. Using capillary electrophoresis with amperometric detection, epicatechin and catechin were detected in all of the seven Cynomorium samples collected in different areas

Two anthocyanin pigments  were isolated from the flowering tops of C. coccineum. Cyanidin 3-O-glucoside was identified to be the major pigment (92%), while cyanidin 3-O-rhamnosylglucoside  was identified to be the minor one (8%) . Besides the above mentioned flavan-3-ols and anthocyanins, compounds 20-27 (Fig. 5) of other flavonoid sub-types were isolated or detected in C. songaricum.

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