Structure of PDE3A\u2013SLFN12 complex and structure-based design for a potent apoptosis inducer of tumor cells

Jie Chen,Hong-Wei Wang,Niu Huang,Xiaodong Wang,Qingcui Wu,Yuxing Sun,Shuanhu Gao,Yuanxun Wang,Xiangbing Qi,Yinpin Huang,Dianrong Li,Nan Liu

doi:10.1038/s41467-021-26546-8

Abstract

Molecular glues are a class of small molecular drugs that mediate protein-protein interactions, that induce either the degradation or stabilization of target protein. A structurally diverse group of chemicals, including 17-β-estradiol (E2), anagrelide, nauclefine, and DNMDP, induces apoptosis by forming complexes with phosphodiesterase 3A (PDE3A) and Schlafen 12 protein (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. In this work, we report the high-resolution cryo-electron microscopy structure of PDE3A-SLFN12 complexes isolated from cultured HeLa cells 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. The resulting small molecule-modified interface binds to the short helix (E552-I558) of SLFN12 through hydrophobic interactions, thus “gluing” the two proteins together. Based on the complex structure, we designed and synthesized analogs of anagrelide, a known drug used for the treatment of thrombocytosis, to enhance their interactions with SLFN12, and achieved superior efficacy in inducing apoptosis in cultured cells as well as in tumor xenografts.

Highlights

Molecular glues are a class of small molecular drugs that mediate protein-protein interactions, that induce either the degradation or stabilization of target protein
Our truncation experiments revealed that the patch of residues 669-679 of phosphodiesterase 3A (PDE3A) is responsible for the PDE3A sensitivity to these small molecules treatment (Fig. 3a), which is located rather far away from the catalytic and enzymatic site, i.e., the moleculebinding site
This probably suggests some allosteric interactions of the N-terminal domain that are required for the proper functioning of PDE3A

Summary

Introduction

Molecular glues are a class of small molecular drugs that mediate protein-protein interactions, that induce either the degradation or stabilization of target protein. A structurally diverse group of chemicals, including 17-β-estradiol (E2), anagrelide, nauclefine, and DNMDP, induces apoptosis by forming complexes with phosphodiesterase 3A (PDE3A) and Schlafen 12 protein (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. PDE3A is a phosphodiesterase that catalyzes the hydrolysis of cyclic adenosine monophosphate (cAMP) or cyclic guanosine monophosphate (cGMP)[4] It appears in three isoforms in cells, each with the distinctive N-terminal regulator domain originating from alternative usage of the start codon, and a common C-terminal catalytic domain[5]. Human SLFN14 mutations underlie thrombocytopenia with excessive bleeding and platelet secretion defects but the molecular mechanism for such a defect is not known[16]

Methods

Results

Conclusion