{"doi":"10.1101/2025.04.22.649986","title":"Discovery of RNA-Reactive Small Molecules Guides Design of Electrophilic Modules for RNA-Specific Covalent Binders","abstract":"Abstract RNA is a key drug target that can be modulated by small molecules, however covalent binders of RNA remain largely unexplored. Using a high-throughput mass spectrometry screen of 2,000 electrophilic compounds, we identified ligands that react with RNA in a binding-dependent manner. RNA reactivity was influenced by both the reactive group and the RNA-binding scaffold. Electrophilic modules such as 3-chloropivalamide, bis(2-chloroethyl)amine, chloroacetamide, and N-acylimidazole that react with proteins also cross-linked to RNA, especially when paired with aromatic heterocycles, particularly those with a thieno[3,2-c]pyridinium core. These results suggest that electrophiles commonly used for protein targeting can also covalently modify RNA, potentially contributing to both on- and off-target effects. This insight enabled the design of an RNA-specific covalent compound by modifying a Hoechst scaffold, originally identified to bind DNA, to react selectively with the expanded triplet repeat RNA, r(CUG) exp , that causes myotonic dystrophy type 1 (DM1). Selectivity appears to arise from binding to the RNA major groove near the reactive site. Overall, this study highlights the potential of rationally designing covalent RNA-targeting small molecules. TOC Graphic","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":555495,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9525,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":804221,"name":"Patrick R. A. Zanon","orcid":"0000-0002-8883-8275","position":1,"is_corresponding":false},{"id":712050,"name":"Amirhossein Taghavi","orcid":"0000-0001-9270-9145","position":2,"is_corresponding":false},{"id":1380865,"name":"Kisu Sung","orcid":"0000-0002-2012-2502","position":3,"is_corresponding":false},{"id":249561,"name":"Matthew D. Disney","orcid":"0000-0001-8486-1796","position":4,"is_corresponding":false},{"id":244754,"name":"Noah A. Springer","orcid":"0000-0001-8868-0415","position":0,"is_corresponding":true}],"reference_count":104,"raw_metadata":null,"created_at":"2026-07-19T02:54:59.329539Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}