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Small molecules that target group II introns are potent antifungal agents

Abstract

Specific RNA structures control numerous metabolic processes that impact human health, and yet efforts to target RNA structures de novo have been limited. In eukaryotes, the self-splicing group II intron is a mitochondrial RNA tertiary structure that is absent in vertebrates but essential for respiration in plants, fungi and yeast. Here we show that this RNA can be targeted through a process of high-throughput in vitro screening, SAR and lead optimization, resulting in high-affinity compounds that specifically inhibit group IIB intron splicing in vitro and in vivo and lack toxicity in human cells. The compounds are potent growth inhibitors of the pathogen Candida parapsilosis, displaying antifungal activity comparable to that of amphotericin B. These studies demonstrate that RNA tertiary structures can be successfully targeted de novo, resulting in pharmacologically valuable compounds.

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Fig. 1: The assays for compound development.
Fig. 2: Summary of SAR studies on compound 1.
Fig. 3: Active compounds selectively inhibit group II splicing in vivo.
Fig. 4: Active compounds selectively inhibit group II splicing in vitro.

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Authors can confirm that all relevant data are included in the paper and/or its supplementary information files.

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Acknowledgements

We thank S. Umlauf, P. Gareiss and J. Merkel at Yale Center for Molecular Discovery for their help with high-throughput screening. We are grateful to K. Blount and R. Breaker for help with setting up MIC experiments. We thank J. Sinclair and A. Schepartz for sharing their expertise on cytotoxicity experiments. We gratefully acknowledge T. Fox (Cornell University) for sharing wild-type and mtDNA intronless S. cerevisiae strains. We thank S. Woodson (Johns Hopkins Unversity) for sharing the Azo-pre-tRNA plasmid. We thank D. Chenoweth and A. DeBerardinis for helpful discussions. We are grateful to S. Herzon and R. Breaker for comments on the manuscript. We are grateful to C. Zhao for help in making Supplementary Fig. 1. A.M.P. is an Investigator, and O.F is a Research Specialist in the Howard Hughes Medical Institute. This work was supported by NIH grants RO1GM50313 to A.M.P. and R43 AI115951 to M.V.Z.

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A.M.P., O.F. and G.E.J. designed the study. All authors contributed to this work as follows: O.F. performed in vitro biochemical studies of splicing inhibition, carried out cytotoxicity and MIC experiments; G.E.J. designed small-molecule inhibitors and carried out organic synthesis of small molecules; R.L.A. performed in vivo splicing inhibition experiments in S. cerevisiae and C. parapsilosis; L.Y. performed organic synthesis of small molecules; M.C.V.Z. designed small-molecule inhibitors; A.M.P., O.F., G.E.J. and R.L.A. wrote the paper.

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Correspondence to Anna Marie Pyle.

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Fedorova, O., Jagdmann, G.E., Adams, R.L. et al. Small molecules that target group II introns are potent antifungal agents. Nat Chem Biol 14, 1073–1078 (2018). https://doi.org/10.1038/s41589-018-0142-0

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