Structure of PDE3A-SLFN12 and Structure-based Design for Ptent Apoptosis Inducer of Tumor Cells

A structurally diverse group of chemicals, including female sex hormone 17-β-estradiol (E2), a clinically used anti-platelet drug anagrelide, a natural product nauclefine, and a synthetic chemical 6-(4-(diethylamino)-3-nitrophenyl)-5-methyl-4,5-dihydropyridazin-3(2<em>H</em>)-one, DNMDP, induce apoptosis by forming a complex with phosphodiesterase 3A (PDE3A) and Schlafen 12 (SLFN12). They do so by binding to the PDE3A enzymatic pocket that allows the compound-bound PDE3A to recruit and stabilize SLFN12, which in turn blocks protein translation, leading to apoptosis. We report here the high-resolution cryo-EM structure of PDE3A-SLFN12 complexes isolated from the cultured HeLa cells, which were pre-treated with either anagrelide, or nauclefine, or DNMDP. The PDE3A-SLFN12 complexes exhibit a butterfly-like shape, forming a heterotetramer with these small molecules, which are packed in a shallow pocket in the catalytic domain of PDE3A, and the resulting modified interface binds with the short helix (E552-I558) of SLFN12 through hydrophobic interactions. Based on this structural information, we designed and synthesized anagrelide analogs to enhance their interactions with SLFN12 and thus achieved superior efficacy in inducing apoptosis in cultured cells as well as tumor xenograft. Our results demonstrated that by enhancing the compound-mediated ‘glue” interaction between PDE3A and SLFN12, more potent apoptosis inducers with potential superior anti-cancer activity can be achieved.