{"doi":"10.1038/s42003-024-06584-w","title":"A ligand discovery toolbox for the WWE domain family of human E3 ligases","abstract":"Abstract The WWE domain is a relatively under-researched domain found in twelve human proteins and characterized by a conserved tryptophan-tryptophan-glutamate (WWE) sequence motif. Six of these WWE domain-containing proteins also contain domains with E3 ubiquitin ligase activity. The general recognition of poly-ADP-ribosylated substrates by WWE domains suggests a potential avenue for development of Proteolysis-Targeting Chimeras (PROTACs). Here, we present novel crystal structures of the HUWE1, TRIP12, and DTX1 WWE domains in complex with PAR building blocks and their analogs, thus enabling a comprehensive analysis of the PAR binding site structural diversity. Furthermore, we introduce a versatile toolbox of biophysical and biochemical assays for the discovery and characterization of novel WWE domain binders, including fluorescence polarization-based PAR binding and displacement assays, 15 N-NMR-based binding affinity assays and 19 F-NMR-based competition assays. Through these assays, we have characterized the binding of monomeric iso -ADP-ribose ( iso -ADPr) and its nucleotide analogs with the aforementioned WWE proteins. Finally, we have utilized the assay toolbox to screen a small molecule fragment library leading to the successful discovery of novel ligands targeting the HUWE1 WWE domain.","journal":"Communications Biology","year":2024,"id":466014,"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":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9474,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1025944,"name":"Serah Kimani","orcid":"0000-0002-6960-3833","position":1,"is_corresponding":false},{"id":1297831,"name":"Milan M. Fowkes","orcid":"0000-0003-3373-7714","position":2,"is_corresponding":false},{"id":462754,"name":"Aiping Dong","orcid":null,"position":3,"is_corresponding":false},{"id":167489,"name":"Hong Zheng","orcid":null,"position":4,"is_corresponding":false},{"id":805418,"name":"Yanjun Li","orcid":"0000-0002-9512-5265","position":5,"is_corresponding":false},{"id":344019,"name":"Morgan Dasovich","orcid":"0000-0001-7951-9662","position":6,"is_corresponding":false},{"id":863291,"name":"Krzysztof M. Żak","orcid":"0000-0001-5844-6599","position":7,"is_corresponding":false},{"id":236295,"name":"Anthony K. L. Leung","orcid":"0000-0001-5569-4036","position":8,"is_corresponding":false},{"id":1178775,"name":"Jonathan M. Elkins","orcid":"0000-0003-2858-8929","position":9,"is_corresponding":false},{"id":853141,"name":"Dirk Kessler","orcid":"0000-0001-6808-9011","position":10,"is_corresponding":false},{"id":84362,"name":"C.H. Arrowsmith","orcid":"0000-0002-4971-3250","position":11,"is_corresponding":false},{"id":277395,"name":"Levon Halabelian","orcid":"0000-0003-4361-3619","position":12,"is_corresponding":false},{"id":853950,"name":"Jark Böttcher","orcid":null,"position":13,"is_corresponding":false},{"id":1298268,"name":"Lena Münzker","orcid":null,"position":0,"is_corresponding":true}],"reference_count":74,"raw_metadata":null,"created_at":"2026-07-19T02:04:54.606394Z","pmid":"39048679","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":[]}