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Estrogen acts by binding to its receptors, termed as ERs. The binding brings two ERs together (homo- or heterodimerization with cognate ER proteins) along with coregulatory proteins which suppress or activate gene transcription by the complex, eventually leading to a physiological or sometimes pathological response. By acting on this system, enterolactone may offer a natural selective estrogen-receptor modulator (SERM) type effect. Thus by binding the estrogen receptor in different target tissues, enterolactone may bring about agonist or antagonist type response, depending on the availability and recruitment of tissue specific co-regulatory proteins to the estrogen receptor signalling complex. Therefore, and depending on the concentration of endogenous estradiol and the distribution of estrogen receptors, enterolactone may act as either an estrogen receptor (ER) agonist or as an estrogen antagonist. When estrogen levels fall enterolactone may exert a weak estrogen-like effect (mimicking the presence of estrogen), when estrogen levels are high enterolactone occupies and block estrogen receptors thus acting to smooth the peaks and troughs.

Importantly, the estrogenic activity of enterolactone is relatively weak and therefore the risk of unwanted effects due to adverse estrogenicity is minimal.