A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex

  • Cell Chem Biol. 2021 Aug 19;28(8):1145-1157.e6. doi: 10.1016/j.chembiol.2021.02.007.
Rakesh Chatrikhi  1 ,  Callen F Feeney  1 ,  Mary J Pulvino  1 ,  Georgios Alachouzos  2 ,  Andrew J MacRae  3 ,  Zackary Falls  4 ,  Sumit Rai  5 ,  William W Brennessel  2 ,  Jermaine L Jenkins  1 ,  Matthew J Walter  6 ,  Timothy A Graubert  5 ,  Ram Samudrala  4 ,  Melissa S Jurica  3 ,  Alison J Frontier  2 ,  Clara L Kielkopf  7
Affiliations
  • 1. Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14620, USA.
  • 2. Department of Chemistry, University of Rochester, Rochester, NY 14627, USA.
  • 3. Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
  • 4. Department of Medical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14214, USA.
  • 5. Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02114, USA.
  • 6. Department of Medicine, Washington University, St. Louis, MO 63110, USA.
  • 7. Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14620, USA. Electronic address: [email protected].
PMID: 33689684 DOI: 10.1016/j.chembiol.2021.02.007
Abstract

Dysregulated pre-mRNA splicing is an emerging Achilles heel of cancers and myelodysplasias. To expand the currently limited portfolio of small-molecule drug leads, we screened for chemical modulators of the U2AF complex, which nucleates spliceosome assembly and is mutated in myelodysplasias. A hit compound specifically enhances RNA binding by a U2AF2 subunit. Remarkably, the compound inhibits splicing of representative substrates and stalls spliceosome assembly at the stage of U2AF function. Computational docking, together with structure-guided mutagenesis, indicates that the compound bridges the tandem U2AF2 RNA recognition motifs via hydrophobic and electrostatic moieties. Cells expressing a cancer-associated U2AF1 mutant are preferentially killed by treatment with the compound. Altogether, our results highlight the potential of trapping early spliceosome assembly as an effective pharmacological means to manipulate pre-mRNA splicing. By extension, we suggest that stabilizing assembly intermediates may offer a useful approach for small-molecule inhibition of macromolecular machines.

Keywords
S34F mutant; U2AF(35); U2AF(65); U2AF1; myelodysplastic syndrome; ribonucleoprotein targeting; spliceosome inhibition; splicing factor mutation; therapeutic strategy.
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