RNA is challenging to target with small molecules of low molecular weight, with high affinity and specificity. One of the challenges in the RNA-targeting field is overcoming the perception that compounds that affect disease pathways do not possess favorable physicochemical properties, as compared to known orally bioavailable small molecule medicines. In this study, both a platform and a novel bioactive interaction are developed to address this challenge. Fragment-based drug discovery has enabled the development of small molecules that affect various biological processes. Herein, we designed an RNA-focused small molecule fragment collection (n = 2500) by analyzing features in all known compounds that bind RNA. The RNA binding landscape for each fragment was defined using a library-versus-library selection called two-dimensional combinatorial screen (2DCS). By studying the fragment library for binding to 5,210 three-dimensionally folded RNA structures, 12.8 million interactions were analyzed, defining molecular recognition properties. Mining of this data set across the human transcriptome defined a drug-like fragment that potently and specifically targeted the microRNA-372 hairpin precursor (K<sub>d</sub> = 300 nM; MW = 273 Da; Quantitative Estimate of Drug-likeness (QED) score of 0.8), which was predicted to bind the Dicer processing site of precursor microRNA-372. The compound selectively inhibited the processing of pre-miR-372 at low micromolar concentrations in cancer cells, having limited off-targets across the miRnome, and specifically reversing a miR-372-driven proliferative and invasive phenotype in a gastric cancer cell line. Thus, here we show that fragments should be considered when identifying chemical matter that binds RNA and can provide mechanistically defined small molecules that selectively affect RNA-mediated pathways. Interestingly, the fragment compound described in this study has a QED score of 0.8, which is higher than most RNA binding compounds identified so far and is comparable with the QED scores of orally bioavailable FDA approved small molecule drugs. This is exciting to see that high QED scores and drug like properties are indeed possible for RNA binders which can bind relatively simpler RNA 3D folds, an A bulge with closing AU base pairs in this case. This study, with other fragment-based drug discovery approaches to target RNA, will help accelerate employment of RNA as a pharmaceutical target for small molecules.

Library versus library screening of fragments for binding RNA yields a potent inhibitor of an oncogenic RNA

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ACS Fall 2022

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.