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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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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
OpenAccess logo Genes Dev 32 309-320 (2018)
Cited: 62 times
EuropePMC logo PMID: 29491137

Abstract

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.

Reviews - 5zya mentioned but not cited (1)

  1. Structures of SF3b1 reveal a dynamic Achilles heel of spliceosome assembly: Implications for cancer-associated abnormalities and drug discovery. Maji D, Grossfield A, Kielkopf CL. Biochim Biophys Acta Gene Regul Mech 1862 194440 (2019)

Articles - 5zya mentioned but not cited (5)

  1. Food-Derived Compounds Apigenin and Luteolin Modulate mRNA Splicing of Introns with Weak Splice Sites. Kurata M, Fujiwara N, Fujita KI, Yamanaka Y, Seno S, Kobayashi H, Miyamae Y, Takahashi N, Shibuya Y, Masuda S. iScience 22 336-352 (2019)
  2. Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly. Yang F, Bian T, Zhan X, Chen Z, Xing Z, Larsen NA, Zhang X, Shi Y. Nat Commun 14 897 (2023)
  3. Thiol-disulphide independent in-cell trapping for the identification of peroxiredoxin 2 interactors. Luo T, Pueyo JM, Wahni K, Yvanoff C, Lazar T, Pyr Dit Ruys S, Vertommen D, Ezeriņa D, Messens J. Redox Biol 46 102066 (2021)
  4. SF3B1 modulators affect key genes in metastasis and drug influx: a new approach to fight pancreatic cancer chemoresistance. Randazzo O, Cascioferro SM, Pecoraro C, Iddouch WA, Avan A, Parrino B, Carbone D, Perricone U, Peters GJ, Diana P, Giovannetti E. Cancer Drug Resist 4 904-922 (2021)
  5. Investigating the Molecular Mechanism of H3B-8800: A Splicing Modulator Inducing Preferential Lethality in Spliceosome-Mutant Cancers. Spinello A, Borišek J, Malcovati L, Magistrato A. Int J Mol Sci 22 11222 (2021)


Reviews citing this publication (26)

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Articles citing this publication (30)

  1. Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia. Wang E, Lu SX, Pastore A, Chen X, Imig J, Chun-Wei Lee S, Hockemeyer K, Ghebrechristos YE, Yoshimi A, Inoue D, Ki M, Cho H, Bitner L, Kloetgen A, Lin KT, Uehara T, Owa T, Tibes R, Krainer AR, Abdel-Wahab O, Aifantis I. Cancer Cell 35 369-384.e7 (2019)
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  7. Elucidation of the aberrant 3' splice site selection by cancer-associated mutations on the U2AF1. Yoshida H, Park SY, Sakashita G, Nariai Y, Kuwasako K, Muto Y, Urano T, Obayashi E. Nat Commun 11 4744 (2020)
  8. Functional analysis of Hsh155/SF3b1 interactions with the U2 snRNA/branch site duplex. Carrocci TJ, Paulson JC, Hoskins AA. RNA 24 1028-1040 (2018)
  9. The pre-mRNA splicing and transcription factor Tat-SF1 is a functional partner of the spliceosome SF3b1 subunit via a U2AF homology motif interface. Loerch S, Leach JR, Horner SW, Maji D, Jenkins JL, Pulvino MJ, Kielkopf CL. J Biol Chem 294 2892-2902 (2019)
  10. Dynamics of the DEAD-box ATPase Prp5 RecA-like domains provide a conformational switch during spliceosome assembly. Beier DH, Carrocci TJ, van der Feltz C, Tretbar US, Paulson JC, Grabowski N, Hoskins AA. Nucleic Acids Res 47 10842-10851 (2019)
  11. LINC01348 suppresses hepatocellular carcinoma metastasis through inhibition of SF3B3-mediated EZH2 pre-mRNA splicing. Lin YH, Wu MH, Liu YC, Lyu PC, Yeh CT, Lin KH. Oncogene 40 4675-4685 (2021)
  12. CRISPR editing of sftb-1/SF3B1 in Caenorhabditis elegans allows the identification of synthetic interactions with cancer-related mutations and the chemical inhibition of splicing. Serrat X, Kukhtar D, Cornes E, Esteve-Codina A, Benlloch H, Cecere G, Cerón J. PLoS Genet 15 e1008464 (2019)
  13. Disclosing the Impact of Carcinogenic SF3b Mutations on Pre-mRNA Recognition Via All-Atom Simulations. Borišek J, Saltalamacchia A, Gallì A, Palermo G, Molteni E, Malcovati L, Magistrato A. Biomolecules 9 E633 (2019)
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  15. Herboxidiene Features That Mediate Conformation-Dependent SF3B1 Interactions to Inhibit Splicing. Gamboa Lopez A, Allu SR, Mendez P, Chandrashekar Reddy G, Maul-Newby HM, Ghosh AK, Jurica MS. ACS Chem Biol 16 520-528 (2021)
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  22. Splicing factor SF3B3, a NS5-binding protein, restricts ZIKV infection by targeting GCH1. Chen T, Yang H, Liu P, Hamiti M, Zhang X, Xu Y, Quan W, Zhang Y, Yu W, Jiao L, Du T, Xi J, Yin B, Zhou W, Lu S, Peng X. Virol Sin 38 222-232 (2023)
  23. Editorial Daedal Facets of Splice Modulator Optimization. Chan WC, León B, Krug KA, Patel A, La Clair JJ, Burkart MD. ACS Med Chem Lett 9 1070-1072 (2018)
  24. Genome-wide evolution of wobble base-pairing nucleotides of branchpoint motifs with increasing organismal complexity. Nguyen H, Das U, Xie J. RNA Biol 17 311-324 (2020)
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