{"doi":"10.1101/2023.06.09.544387","title":"Antibiotic that inhibits <i>trans</i> -translation blocks binding of EF-Tu to tmRNA but not to tRNA","abstract":"ABSTRACT Trans- Translation is conserved throughout bacteria and is essential in many species. High-throughput screening identified a tetrazole-based trans -translation inhibitor, KKL-55, that has broad-spectrum antibiotic activity. A biotinylated version of KKL-55 pulled down Elongation Factor Thermo-unstable (EF-Tu) from bacterial lysates. Purified EF-Tu bound KKL-55 in vitro with a K d = 2 µM, confirming a high-affinity interaction. An X-ray crystal structure showed KKL-55 binds in domain 3 of EF-Tu, and mutation of residues in the binding pocket abolished KKL-55 binding. RNA binding assays in vitro showed that KKL-55 inhibits binding between EF-Tu and tmRNA, but not between EF-Tu and tRNA. These data demonstrate a new mechanism for inhibition of EF-Tu function and suggest that this specific inhibition of EF-Tu•tmRNA binding is a viable target for antibiotic development. IMPORTANCE EF-Tu is a universally conserved translation factor that mediates productive interactions between tRNAs and the ribosome. In bacteria, EF-Tu also delivers tmRNA-SmpB to the ribosome during trans -translation. We report the first small molecule, KKL-55, that specifically inhibits EF-Tu activity in trans -translation without affecting its activity in normal translation. KKL-55 has broad-spectrum antibiotic activity, suggesting that compounds targeted to the tmRNA-binding interface of EF-Tu could be developed into new antibiotics to treat drug-resistant infections.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":408583,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9543,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":506136,"name":"Ha An Nguyen","orcid":"0000-0003-2620-2893","position":1,"is_corresponding":false},{"id":385906,"name":"John N. Alumasa","orcid":"0000-0002-9373-9618","position":2,"is_corresponding":false},{"id":481344,"name":"Alexandra B. Kuzmishin Nagy","orcid":"0000-0002-5976-6890","position":3,"is_corresponding":false},{"id":1080771,"name":"Michael L. Vazquez","orcid":"0000-0001-6244-6540","position":4,"is_corresponding":false},{"id":17817,"name":"Christine M. Dunham","orcid":"0000-0002-8821-688X","position":5,"is_corresponding":false},{"id":332645,"name":"Kenneth C. Keiler","orcid":"0000-0001-8753-335X","position":6,"is_corresponding":false},{"id":1080770,"name":"Neeraja Marathe","orcid":"0009-0003-6314-0254","position":0,"is_corresponding":true}],"reference_count":44,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T01:21:18.414003Z","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":[]}