Targeting oncogenic transcriptional corepressor Nac1 POZ domain with conformationally constrained peptides by cyclization and stapling
Targeting oncogenic transcriptional corepressor Nac1 POZ domain with conformationally constrained peptides by cyclization and stapling
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通过环化和装订用构象限制肽靶向致癌转录辅阻遏物 Nac1 POZ 结构域
DOI：
10.1016/j.bioorg.2018.05.024
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发表时间：
2018
影响因子：
5.1
通讯作者：
Lv Fenglin
中科院分区：
文献类型：
--
作者：
Wu Tao;He Ping;Wu Wei;Chen Yingli;Lv Fenglin
致癌转录辅阻遏物 Nac1 包含保守的 POZ 蛋白-蛋白相互作用模块，可介导与其自身或其他 POZ 蛋白的同二聚化或异二聚化。二聚化已被认为是癌症治疗的一个有吸引力的靶标。在这里，我们试图（i）发现人类基因组中 Nac1 的潜在结合伙伴，（ii）从 Nac1 与其假定伙伴的复杂界面中衍生关键肽段，以及（iii）提高肽与 Nac1 POZ 结构域的结合亲和力。在此过程中，在原子水平上对具有 136 个人类 POZ 结构域的 Nac1 POZ 二聚化进行了建模、模拟和分析，以阐明结构基础、能量性质和动力学行为。确定了二聚化界面上的两个热点区域，即 α1-螺旋和 α2/α3-发夹，它们负责稳定形成的 POZ-POZ 二聚体复合物。将α1-螺旋和α2/α3-发夹从界面上剥离，得到各自分离的SIP肽，然而，它们在游离状态下表现出很大的灵活性和内在无序性，因此在重新结合到Nac1 POZ结构域时会产生相当大的损失。通过仔细检查蛋白质背景下α1-螺旋和α2/α3-发夹的天然折叠结构及其与结构域的相互作用模式，我们为这两个肽分别合理地设计了烃桥和二硫键，以限制其在自由状态下的构象灵活性，从而在很大程度上减少了灵活性损失。因此，源自Nac1、Miz1和Slx4的三个α1-螺旋肽通过全烃桥钉合，而源自Nac1、Bacd1、Klh28和Mynn的四个α2/α3-发夹肽通过二硫键环化。结合亲和力分析表明，按照设计，这些肽在装订和环化时从非或弱结合物转化为 Nac1 POZ 结构域的中等或良好结合物。
The oncogenic transcriptional corepressor Nac1 contains a conserved POZ protein–protein interaction module that mediates homodimerization or heterodimerization with itself or other POZ proteins. The dimerization has been recognized as an attractive target for cancer therapy. Here, we attempted to (i) discover those potential binding partners of Nac1 in the human genome, (ii) derive key peptide segments from the complex interface of Nac1 with its putative partners, and (iii) improve the peptide binding affinity to Nac1 POZ domain. In the procedure, Nac1 POZ dimerization with 136 human POZ domains was modeled, simulated and analyzed at atomic level to elucidate structural basis, energetic property and dynamics behavior. Two hotspot regions, namely α1-helix and α2/α3-hairpin, at the dimerization interface were identified that are responsible for stabilizing the formed POZ–POZ dimer complexes. The α1-helix and α2/α3-hairpin were stripped from the interface to derive their respective isolated SIP peptides, which, however, exhibited a large flexibility and intrinsic disorder in free state, and thus would incur a considerable penalty upon rebinding to Nac1 POZ domain. By carefully examining the natively folded structures of α1-helix and α2/α3-hairpin in protein context and their interaction modes with the domain, we rationally designed a hydrocarbon bridge and a disulfide bond separately for the two peptides in order to constrain their conformational flexibility in free state, thus largely minimizing the flexibility penalty. Consequently, three α1-helix peptides derived from Nac1, Miz1 and Slx4 were stapled by all-hydrocarbon bridge, while four α2/α3-hairpin peptides derived from Nac1, Bacd1, Klh28 and Mynn were cyclized by disulfide bond. Binding affinity analysis revealed that, as designed, these peptides were converted from non- or weak binders to moderate or good binders of Nac1 POZ domain upon the stapling and cyclization.