SANT-2 is primarily used in biochemical and pharmacological research as a selective antagonist of the Smoothened (SMO) receptor, which is a key component of the Hedgehog (Hh) signaling pathway. This pathway plays a critical role in embryonic development, tissue homeostasis, and cancer progression. By inhibiting SMO, SANT-2 effectively suppresses aberrant Hedgehog signaling, making it a valuable tool for studying pathway mechanisms and validating therapeutic targets.

It is commonly applied in cancer research, particularly in models of basal cell carcinoma, medulloblastoma, and other tumors driven by Hedgehog pathway activation. Researchers use SANT-2 to probe the effects of pathway inhibition on cell proliferation, differentiation, and apoptosis. Due to its selectivity, it helps distinguish SMO-dependent effects from off-target actions in experimental settings.

SANT-2 is also used to compare the efficacy and mechanism of action with other SMO inhibitors, aiding in the development of improved anti-cancer agents. Its application remains largely confined to in vitro and preclinical in vivo studies, serving as a research probe rather than a therapeutic agent.