Live Cell Screening to Identify RNA-binding Small Molecule Inhibitors of the Pre-let-7-Lin28 RNA-protein Interaction

Overview

Journal RSC Med Chem

Publisher Royal Society of Chemistry

Specialty Chemistry

Date 2024 May 24

PMID 38784453

Authors

Sydney L Rosenblum

Dalia M Soueid

George Giambasu

Steve Vander Roest

Alexander Pasternak

Erin F DiMauro

Vladimir Simov

Amanda L Garner

Affiliations

Soon will be listed here.

Abstract

Dysregulation of the networking of RNA-binding proteins (RBPs) and RNAs drives many human diseases, including cancers, and the targeting of RNA-protein interactions (RPIs) has emerged as an exciting area of RNA-targeted drug discovery. Accordingly, methods that enable the discovery of cell-active small molecule modulators of RPIs are needed to propel this emerging field forward. Herein, we describe the application of live-cell assay technology, RNA interaction with protein-mediated complementation assay (RiPCA), for high-throughput screening to identify small molecule inhibitors of the pre-let-7d-Lin28A RPI. Utilizing a combination of RNA-biased small molecules and virtual screening hits, we discovered an RNA-binding small molecule that can disrupt the pre-let-7-Lin28 interaction demonstrating the potential of RiPCA for advancing RPI-targeted drug discovery.

Citing Articles

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References

Hirai H, Iwasawa Y, Okada M, Arai T, Nishibata T, Kobayashi M . Small-molecule inhibition of Wee1 kinase by MK-1775 selectively sensitizes p53-deficient tumor cells to DNA-damaging agents. Mol Cancer Ther. 2009; 8(11):2992-3000. DOI: 10.1158/1535-7163.MCT-09-0463. View

Gi Byun W, Lim D, Park S . Discovery of Small-Molecule Modulators of Protein-RNA Interactions by Fluorescence Intensity-Based Binding Assay. Chembiochem. 2019; 21(6):818-824. DOI: 10.1002/cbic.201900467. View

Friesner R, Murphy R, Repasky M, Frye L, Greenwood J, Halgren T . Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem. 2006; 49(21):6177-96. DOI: 10.1021/jm051256o. View

Mastracchio A, Lai C, Torrent M, Bromberg K, Buchanan F, Ferguson D . Investigation of biaryl heterocycles as inhibitors of Wee1 kinase. Bioorg Med Chem Lett. 2019; 29(12):1481-1486. DOI: 10.1016/j.bmcl.2019.04.017. View

Halgren T, Murphy R, Friesner R, Beard H, Frye L, Pollard W . Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem. 2004; 47(7):1750-9. DOI: 10.1021/jm030644s. View

Roush S, Slack F . The let-7 family of microRNAs. Trends Cell Biol. 2008; 18(10):505-16. DOI: 10.1016/j.tcb.2008.07.007. View

Jankowsky E, Harris M . Specificity and nonspecificity in RNA-protein interactions. Nat Rev Mol Cell Biol. 2015; 16(9):533-44. PMC: 4744649. DOI: 10.1038/nrm4032. View

Viswanathan S, Powers J, Einhorn W, Hoshida Y, Ng T, Toffanin S . Lin28 promotes transformation and is associated with advanced human malignancies. Nat Genet. 2009; 41(7):843-8. PMC: 2757943. DOI: 10.1038/ng.392. View

Tsanov K, Pearson D, Wu Z, Han A, Triboulet R, Seligson M . LIN28 phosphorylation by MAPK/ERK couples signalling to the post-transcriptional control of pluripotency. Nat Cell Biol. 2016; 19(1):60-67. PMC: 5182091. DOI: 10.1038/ncb3453. View

10.

Lim D, Gi Byun W, Koo J, Park H, Park S . Discovery of a Small-Molecule Inhibitor of Protein-MicroRNA Interaction Using Binding Assay with a Site-Specifically Labeled Lin28. J Am Chem Soc. 2016; 138(41):13630-13638. DOI: 10.1021/jacs.6b06965. View

11.

Wang T, Wang G, Hao D, Liu X, Wang D, Ning N . Aberrant regulation of the LIN28A/LIN28B and let-7 loop in human malignant tumors and its effects on the hallmarks of cancer. Mol Cancer. 2015; 14:125. PMC: 4512107. DOI: 10.1186/s12943-015-0402-5. View

12.

Van Nostrand E, Freese P, Pratt G, Wang X, Wei X, Xiao R . A large-scale binding and functional map of human RNA-binding proteins. Nature. 2020; 583(7818):711-719. PMC: 7410833. DOI: 10.1038/s41586-020-2077-3. View

13.

Nam Y, Chen C, Gregory R, Chou J, Sliz P . Molecular basis for interaction of let-7 microRNAs with Lin28. Cell. 2011; 147(5):1080-91. PMC: 3277843. DOI: 10.1016/j.cell.2011.10.020. View

14.

Lorenz D, Kaur T, Kerk S, Gallagher E, Sandoval J, Garner A . Expansion of cat-ELCCA for the Discovery of Small Molecule Inhibitors of the Pre-let-7-Lin28 RNA-Protein Interaction. ACS Med Chem Lett. 2018; 9(6):517-521. PMC: 6004563. DOI: 10.1021/acsmedchemlett.8b00126. View

15.

Spallarossa A, Tasso B, Russo E, Villa C, Brullo C . The Development of FAK Inhibitors: A Five-Year Update. Int J Mol Sci. 2022; 23(12). PMC: 9223874. DOI: 10.3390/ijms23126381. View

16.

Palmer B, Smaill J, Rewcastle G, Dobrusin E, Kraker A, Moore C . Structure-activity relationships for 2-anilino-6-phenylpyrido[2,3-d]pyrimidin-7(8H)-ones as inhibitors of the cellular checkpoint kinase Wee1. Bioorg Med Chem Lett. 2005; 15(7):1931-5. DOI: 10.1016/j.bmcl.2005.01.079. View

17.

Viswanathan S, Daley G, Gregory R . Selective blockade of microRNA processing by Lin28. Science. 2008; 320(5872):97-100. PMC: 3368499. DOI: 10.1126/science.1154040. View

18.

Halgren T . Identifying and characterizing binding sites and assessing druggability. J Chem Inf Model. 2009; 49(2):377-89. DOI: 10.1021/ci800324m. View

19.

Wang L, Nam Y, Lee A, Yu C, Roth K, Chen C . LIN28 Zinc Knuckle Domain Is Required and Sufficient to Induce let-7 Oligouridylation. Cell Rep. 2017; 18(11):2664-2675. DOI: 10.1016/j.celrep.2017.02.044. View

20.

Wang L, Rowe R, Jaimes A, Yu C, Nam Y, Pearson D . Small-Molecule Inhibitors Disrupt let-7 Oligouridylation and Release the Selective Blockade of let-7 Processing by LIN28. Cell Rep. 2018; 23(10):3091-3101. PMC: 6511231. DOI: 10.1016/j.celrep.2018.04.116. View