Abstract
Oligonucleotides are designed to target RNA using base pairing rules, but they can be hampered by poor cellular delivery and nonspecific stimulation of the immune system. Small molecules are preferred as lead drugs or probes but cannot be designed from sequence. Herein, we describe an approach termed Inforna that designs lead small molecules for RNA from solely sequence. Inforna was applied to all human microRNA hairpin precursors, and it identified bioactive small molecules that inhibit biogenesis by binding nuclease-processing sites (44% hit rate). Among 27 lead interactions, the most avid interaction is between a benzimidazole (1) and precursor microRNA-96. Compound 1 selectively inhibits biogenesis of microRNA-96, upregulating a protein target (FOXO1) and inducing apoptosis in cancer cells. Apoptosis is ablated when FOXO1 mRNA expression is knocked down by an siRNA, validating compound selectivity. Markedly, microRNA profiling shows that 1 only affects microRNA-96 biogenesis and is at least as selective as an oligonucleotide.
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Acknowledgements
We thank B. White (Department of Cell Biology, University of Connecticut Health Center) for the luciferase plasmids containing FOXO1 3′ UTRs; C. Haga for assistance designing qRT-PCR primers; K. Lowe for assistance with flow cytometry; S. Seedhouse for preliminary studies with Inforna; B. Liu, J. Sokolow and T. Tran for compiling the secondary structures of the miRNA precursors and the RNA motif–small molecule database; and J. Childs-Disney, T. Kodadek, J. Cleveland, B. Roush, J. Joyce, M. Burkard and M. Guo for critical review of the manuscript. This work was funded by the US National Institutes of Health (R01GM097455). M.D.D. is a Camille and Henry Dreyfus Teacher-Scholar.
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S.P.V. designed and completed all of the experiments and contributed to the writing of the manuscript; S.M.G. programmed Inforna; and M.D.D. conceived Inforna, designed experiments and wrote the manuscript.
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Velagapudi, S., Gallo, S. & Disney, M. Sequence-based design of bioactive small molecules that target precursor microRNAs. Nat Chem Biol 10, 291–297 (2014). https://doi.org/10.1038/nchembio.1452
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DOI: https://doi.org/10.1038/nchembio.1452
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