The cryo-EM structure of the SF3b spliceosome complex bound to a splicing modulator reveals a pre-mRNA substrate competitive mechanism of action.
The cryo-EM structure of the SF3b spliceosome complex bound to a splicing modulator reveals a pre-mRNA substrate competitive mechanism of action.
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DOI：
10.1101/gad.311043.117
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发表时间：
2018-02-01
影响因子：
10.5
通讯作者：
Larsen NA
中科院分区：
文献类型：
--
作者：
Finci LI;Zhang X;Huang X;Zhou Q;Tsai J;Teng T;Agrawal A;Chan B;Irwin S;Karr C;Cook A;Zhu P;Reynolds D;Smith PG;Fekkes P;Buonamici S;Larsen NA
在本研究中，Finci et.艾尔给出了U2 SnRNP的一部分SF3B亚复合体(SF3B1、SF3B3、PHF5A和SF3B5)的冷冻EM结构，该结构在3.95 A时与E7107结合。该结构表明了一种剪接调节剂干扰分支点腺苷识别的模型，并支持底物竞争的作用机制。剪接体蛋白的体细胞突变导致RNA剪接失调，并在多种癌症中观察到。这些基因异常可能为靶向治疗提供一个潜在的干预点。SF3B1是U2小核RNP(SnRNP)的一部分，是剪接调节剂的靶点，包括第一个进入临床试验的E7107，以及最近的H3B-8800。调控剪接代表着药物发现中的一流机会，阐明作用模式的结构基础为基于结构的药物设计开辟了新的可能性。在这里，我们提出了SF3B亚复合体(SF3B1、SF3B3、PHF5A和SF3B5)在3.95？时与E7107结合的低温电子显微镜(Cryo-EM)结构。这种结构表明E7107与分支点腺苷结合口袋结合，与导致突变产生抗性的关键残基SF3B1R1074H和PHF5AY36C形成密切接触。该结构提出了一种剪接调节器干扰分支点腺苷识别的模型，并支持底物竞争作用机制(MOA)。使用几个相关的化学探针，我们验证了化合物的姿势，并通过比较它们对强和弱前-mRNA底物的活性来支持它们的底物竞争性MOA。最后，我们提供了PHF5AR38C突变的功能数据和构效关系(SAR)，该突变使细胞对一些化学探针敏感，但对其他化学探针不敏感。开发小分子剪接调节剂代表了一种很有前途的治疗各种疾病的方法，这项工作为这些精致的天然产物进行基于结构的药物设计提供了重要的一步。重要的是，这项工作还表明，低温EM在药物发现中的应用正在成熟。
In this study, Finci et. al. present the cryo-EM structure of the SF3b subcomplex (SF3B1, SF3B3, PHF5A, and SF3B5), part of the U2 snRNP, bound to E7107 at 3.95 A. The structure suggests a model in which splicing modulators interfere with branch point adenosine recognition and supports a substrate competitive mechanism of action. Somatic mutations in spliceosome proteins lead to dysregulated RNA splicing and are observed in a variety of cancers. These genetic aberrations may offer a potential intervention point for targeted therapeutics. SF3B1, part of the U2 small nuclear RNP (snRNP), is targeted by splicing modulators, including E7107, the first to enter clinical trials, and, more recently, H3B-8800. Modulating splicing represents a first-in-class opportunity in drug discovery, and elucidating the structural basis for the mode of action opens up new possibilities for structure-based drug design. Here, we present the cryogenic electron microscopy (cryo-EM) structure of the SF3b subcomplex (SF3B1, SF3B3, PHF5A, and SF3B5) bound to E7107 at 3.95 Å. This structure shows that E7107 binds in the branch point adenosine-binding pocket, forming close contacts with key residues that confer resistance upon mutation: SF3B1R1074H and PHF5AY36C. The structure suggests a model in which splicing modulators interfere with branch point adenosine recognition and supports a substrate competitive mechanism of action (MOA). Using several related chemical probes, we validate the pose of the compound and support their substrate competitive MOA by comparing their activity against both strong and weak pre-mRNA substrates. Finally, we present functional data and structure–activity relationship (SAR) on the PHF5AR38C mutation that sensitizes cells to some chemical probes but not others. Developing small molecule splicing modulators represents a promising therapeutic approach for a variety of diseases, and this work provides a significant step in enabling structure-based drug design for these elaborate natural products. Importantly, this work also demonstrates that the utilization of cryo-EM in drug discovery is coming of age.
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影响因子：
64.8
作者：
Ellis, Matthew J.;Ding, Li;Shen, Dong;Luo, Jingqin;Suman, Vera J.;Wallis, John W.;Van Tine, Brian A.;Hoog, Jeremy;Goiffon, Reece J.;Goldstein, Theodore C.;Ng, Sam;Lin, Li;Crowder, Robert;Snider, Jacqueline;Ballman, Karla;Weber, Jason;Chen, Ken;Koboldt, Daniel C.;Kandoth, Cyriac;Schierding, William S.;McMichael, Joshua F.;Miller, Christopher A.;Lu, Charles;Harris, Christopher C.;McLellan, Michael D.;Wendl, Michael C.;DeSchryver, Katherine;Allred, D. Craig;Esserman, Laura;Unzeitig, Gary;Margenthaler, Julie;Babiera, G. V.;Marcom, P. Kelly;Guenther, J. M.;Leitch, Marilyn;Hunt, Kelly;Olson, John;Tao, Yu;Maher, Christopher A.;Fulton, Lucinda L.;Fulton, Robert S.;Harrison, Michelle;Oberkfell, Ben;Du, Feiyu;Demeter, Ryan;Vickery, Tammi L.;Elhammali, Adnan;Piwnica-Worms, Helen;McDonald, Sandra;Watson, Mark;Dooling, David J.;Ota, David;Chang, Li-Wei;Bose, Ron;Ley, Timothy J.;Piwnica-Worms, David;Stuart, Joshua M.;Wilson, Richard K.;Mardis, Elaine R.
通讯作者：
Mardis, Elaine R.
影响因子：
5.3
作者：
Agafonov, Dmitry E.;Deckert, Jochen;Luehrmann, Reinhard
通讯作者：
Luehrmann, Reinhard
影响因子：
2.2
作者：
Kong Y;Krauthammer M;Halaban R
通讯作者：
Halaban R
影响因子：
3.4
作者：
Hong, D. S.;Kurzrock, R.;LoRusso, P.
通讯作者：
LoRusso, P.
影响因子：
4.8
作者：
Effenberger, Kerstin A.;Anderson, David D.;Jurica, Melissa S.
通讯作者：
Jurica, Melissa S.