{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T03:32:51Z","timestamp":1792467171326,"version":"4.5.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2024,3,30]],"date-time":"2024-03-30T00:00:00Z","timestamp":1711756800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001677","name":"INSERM","doi-asserted-by":"publisher","award":["COPOC2021 MAT-API-00785-A-01"],"award-info":[{"award-number":["COPOC2021 MAT-API-00785-A-01"]}],"id":[{"id":"10.13039\/501100001677","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004099","name":"Ligue contre le cancer","doi-asserted-by":"publisher","award":["APPARN2021.LCC\/SeC"],"award-info":[{"award-number":["APPARN2021.LCC\/SeC"]}],"id":[{"id":"10.13039\/501100004099","id-type":"DOI","asserted-by":"publisher"}]},{"name":"F\u00e9d\u00e9ration de la Recherche M\u00e9dicale","award":["AJE202310017978"],"award-info":[{"award-number":["AJE202310017978"]}]},{"name":"NCCR RNA and Disease","award":["51NF40-182880"],"award-info":[{"award-number":["51NF40-182880"]}]},{"name":"Skyhawk Therapeutics"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Pharmacological modulation of RNA splicing by small molecules is an emerging facet of drug discovery. In this context, the SMN2 splicing modifier SMN-C5 was used as a prototype to understand the mode of action of small molecule splicing modifiers and propose the concept of 5\u2032-splice site bulge repair. In this study, we combined in vitro binding assays and structure determination by NMR spectroscopy to identify the binding modes of four other small molecule splicing modifiers that switch the splicing of either the SMN2 or the HTT gene. Here, we determined the solution structures of risdiplam, branaplam, SMN-CX and SMN-CY bound to the intermolecular RNA helix epitope containing an unpaired adenine within the G-2A-1G+1U+2 motif of the 5\u2032-splice site. Despite notable differences in their scaffolds, risdiplam, SMN-CX, SMN-CY and branaplam contact the RNA epitope similarly to SMN-C5, suggesting that the 5\u2032-splice site bulge repair mechanism can be generalised. These findings not only deepen our understanding of the chemical diversity of splicing modifiers that target A-1 bulged 5\u2032-splice sites, but also identify common pharmacophores required for modulating 5\u2032-splice site selection with small molecules.<\/jats:p>","DOI":"10.1093\/nar\/gkae201","type":"journal-article","created":{"date-parts":[[2024,3,30]],"date-time":"2024-03-30T13:49:23Z","timestamp":1711806563000},"page":"4124-4136","source":"Crossref","is-referenced-by-count":30,"title":["The diversity of splicing modifiers acting on A-1 bulged 5\u2032-splice sites reveals rules for rational drug design"],"prefix":"10.1093","volume":"52","author":[{"given":"Florian","family":"Malard","sequence":"first","affiliation":[{"name":"Universit\u00e9 de Bordeaux , Inserm U1212, CNRS UMR5320, ARNA unit, 146 rue L\u00e9o Saignat, 33076 Bordeaux Cedex, France"},{"name":"Institut Europ\u00e9en de Chimie et Biologie , 2 rue Robert Escarpit, 33607 Pessac Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antje C","family":"Wolter","sequence":"additional","affiliation":[{"name":"ETH Z\u00fcrich, Department of Biology, Institute of Biochemistry , H\u00f6nggerbergring 64, 8093 Z\u00fcrich , Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julien","family":"Marquevielle","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Bordeaux , Inserm U1212, CNRS UMR5320, ARNA unit, 146 rue L\u00e9o Saignat, 33076 Bordeaux Cedex, France"},{"name":"Institut Europ\u00e9en de Chimie et Biologie , 2 rue Robert Escarpit, 33607 Pessac Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Estelle","family":"Morvan","sequence":"additional","affiliation":[{"name":"Institut Europ\u00e9en de Chimie et Biologie, UAR3033 CNRS, Universit\u00e9 de Bordeaux , INSERM US01, Pessac 33600 , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agathe","family":"Ecoutin","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Bordeaux , Inserm U1212, CNRS UMR5320, ARNA unit, 146 rue L\u00e9o Saignat, 33076 Bordeaux Cedex, France"},{"name":"Institut Europ\u00e9en de Chimie et Biologie , 2 rue Robert Escarpit, 33607 Pessac Cedex, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon\u00a0H","family":"R\u00fcdisser","sequence":"additional","affiliation":[{"name":"ETH Z\u00fcrich, Department of Biology, BioNMR platform , H\u00f6nggerbergring 64, 8093 Z\u00fcrich , Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2131-6237","authenticated-orcid":false,"given":"Fr\u00e9d\u00e9ric\u00a0H T","family":"Allain","sequence":"additional","affiliation":[{"name":"ETH Z\u00fcrich, Department of Biology, Institute of Biochemistry , H\u00f6nggerbergring 64, 8093 Z\u00fcrich , Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0094-4760","authenticated-orcid":false,"given":"Sebastien","family":"Campagne","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Bordeaux , Inserm U1212, CNRS UMR5320, ARNA unit, 146 rue L\u00e9o Saignat, 33076 Bordeaux Cedex, France"},{"name":"Institut Europ\u00e9en de Chimie et Biologie , 2 rue Robert Escarpit, 33607 Pessac Cedex, France"},{"name":"ETH Z\u00fcrich, Department of Biology, Institute of Biochemistry , H\u00f6nggerbergring 64, 8093 Z\u00fcrich , Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,3,30]]},"reference":[{"key":"2024050805420836300_B1","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/nrg.2015.3","article-title":"RNA mis-splicing in disease","volume":"17","author":"Scotti","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"2024050805420836300_B2","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1080\/15476286.2022.2100971","article-title":"Principles and correction of 5\u2032-splice site selection","volume":"19","author":"Malard","year":"2022","journal-title":"RNA Biol."},{"key":"2024050805420836300_B3","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1101\/gad.209759.112","article-title":"Pick one, but be quick: 5\u2032 splice sites and the problems of too many choices","volume":"27","author":"Roca","year":"2013","journal-title":"Genes Dev."},{"key":"2024050805420836300_B4","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1016\/0092-8674(83)90432-4","article-title":"The U1 small nuclear RNA-protein complex selectively binds a 5\u2032 splice site in vitro","volume":"33","author":"Mount","year":"1983","journal-title":"Cell"},{"key":"2024050805420836300_B5","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1261\/rna.2040605","article-title":"Determinants of the inherent strength of human 5\u2032 splice sites","volume":"11","author":"Roca","year":"2005","journal-title":"RNA"},{"key":"2024050805420836300_B6","doi-asserted-by":"crossref","first-page":"1012","DOI":"10.1016\/j.molcel.2018.07.033","article-title":"Quantitative activity profile and context dependence of all human 5\u2032 splice sites","volume":"71","author":"Wong","year":"2018","journal-title":"Mol. Cell"},{"key":"2024050805420836300_B7","doi-asserted-by":"crossref","first-page":"194403","DOI":"10.1016\/j.bbagrm.2019.07.004","article-title":"How RNA structure dictates the usage of a critical exon of spinal muscular atrophy gene","volume":"1862","author":"Singh","year":"2019","journal-title":"Biochim. Biophys. Acta Gene Regul. Mech."},{"key":"2024050805420836300_B8","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1146\/annurev.biochem.72.121801.161720","article-title":"Mechanisms of alternative pre-messenger RNA splicing","volume":"72","author":"Black","year":"2003","journal-title":"Annu. Rev. Biochem."},{"key":"2024050805420836300_B9","doi-asserted-by":"crossref","first-page":"4250","DOI":"10.1093\/nar\/gkm402","article-title":"Aberrant 5\u2032 splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization","volume":"35","author":"Buratti","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2024050805420836300_B10","doi-asserted-by":"crossref","first-page":"1098","DOI":"10.1101\/gad.190173.112","article-title":"Widespread recognition of 5\u2032 splice sites by noncanonical base-pairing to U1 snRNA involving bulged nucleotides","volume":"26","author":"Roca","year":"2012","journal-title":"Genes Dev."},{"key":"2024050805420836300_B11","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1101\/gr.6859308","article-title":"Features of 5\u2032-splice-site efficiency derived from disease-causing mutations and comparative genomics","volume":"18","author":"Roca","year":"2008","journal-title":"Genome Res."},{"key":"2024050805420836300_B12","doi-asserted-by":"crossref","first-page":"e2114886119","DOI":"10.1073\/pnas.2114886119","article-title":"Open reading frame correction using splice-switching antisense oligonucleotides for the treatment of cystic fibrosis","volume":"119","author":"Michaels","year":"2022","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2024050805420836300_B13","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1016\/S0140-6736(11)61028-3","article-title":"Exon-skipping therapy for Duchenne muscular dystrophy","volume":"378","author":"Nakamura","year":"2011","journal-title":"Lancet North Am. Ed."},{"key":"2024050805420836300_B14","doi-asserted-by":"crossref","first-page":"1644","DOI":"10.1056\/NEJMoa1813279","article-title":"Patient-customized oligonucleotide therapy for a rare genetic disease","volume":"381","author":"Kim","year":"2019","journal-title":"N. Engl. J. Med."},{"key":"2024050805420836300_B15","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1038\/nature10485","article-title":"Peripheral SMN restoration is essential for long-term rescue of a severe spinal muscular atrophy mouse model","volume":"478","author":"Hua","year":"2011","journal-title":"Nature"},{"key":"2024050805420836300_B16","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1126\/science.1250127","article-title":"SMN2 splicing modifiers improve motor function and longevity in mice with spinal muscular atrophy","volume":"345","author":"Naryshkin","year":"2014","journal-title":"Science"},{"key":"2024050805420836300_B17","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1038\/s41573-021-00162-z","article-title":"Antisense technology: an overview and prospectus","volume":"20","author":"Crooke","year":"2021","journal-title":"Nat. Rev. Drug Discov."},{"key":"2024050805420836300_B18","doi-asserted-by":"crossref","first-page":"7299","DOI":"10.1038\/s41467-021-27157-z","article-title":"Small molecule splicing modifiers with systemic HTT-lowering activity","volume":"12","author":"Bhattacharyya","year":"2021","journal-title":"Nat. Commun."},{"key":"2024050805420836300_B19","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nchembio.1837","article-title":"SMN2 splice modulators enhance U1\u2013pre-mRNA association and rescue SMA mice","volume":"11","author":"Palacino","year":"2015","journal-title":"Nat. Chem. Biol."},{"key":"2024050805420836300_B20","doi-asserted-by":"crossref","first-page":"6501","DOI":"10.1021\/acs.jmedchem.8b00741","article-title":"Discovery of Risdiplam, a Selective Survival of Motor Neuron-2 (SMN2) Gene Splicing Modifier for the Treatment of Spinal Muscular Atrophy (SMA)","volume":"61","author":"Ratni","year":"2018","journal-title":"J. Med. Chem."},{"key":"2024050805420836300_B21","doi-asserted-by":"crossref","first-page":"1476","DOI":"10.1038\/s41467-017-01559-4","article-title":"Binding to SMN2 pre-mRNA-protein complex elicits specificity for small molecule splicing modifiers","volume":"8","author":"Sivaramakrishnan","year":"2017","journal-title":"Nat. Commun."},{"key":"2024050805420836300_B22","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1038\/s41589-019-0384-5","article-title":"Structural basis of a small molecule targeting RNA for a specific splicing correction","volume":"15","author":"Campagne","year":"2019","journal-title":"Nat. Chem. Biol."},{"key":"2024050805420836300_B23","doi-asserted-by":"crossref","first-page":"874","DOI":"10.1021\/acsmedchemlett.0c00659","article-title":"Risdiplam, the First Approved Small Molecule Splicing Modifier Drug as a Blueprint for Future Transformative Medicines","volume":"12","author":"Ratni","year":"2021","journal-title":"ACS Med. Chem. Lett."},{"key":"2024050805420836300_B24","doi-asserted-by":"crossref","first-page":"4444","DOI":"10.1021\/acs.jmedchem.7b00406","article-title":"Discovery of a novel class of survival motor neuron 2 splicing modifiers for the treatment of spinal muscular atrophy","volume":"60","author":"Pinard","year":"2017","journal-title":"J. Med. Chem."},{"key":"2024050805420836300_B25","doi-asserted-by":"crossref","first-page":"6086","DOI":"10.1021\/acs.jmedchem.6b00459","article-title":"Specific correction of alternative survival motor neuron 2 splicing by small molecules: discovery of a potential novel medicine to treat spinal muscular atrophy","volume":"59","author":"Ratni","year":"2016","journal-title":"J. Med. Chem."},{"key":"2024050805420836300_B26","volume-title":"Python 3 Reference Manual","author":"Van\u00a0Rossum","year":"2009"},{"key":"2024050805420836300_B27","article-title":"The compter-aided resonance assignment tutorial","volume-title":"Cantina Verlag","author":"Keller","year":"2004"},{"key":"2024050805420836300_B28","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1007\/s10858-015-9924-9","article-title":"Combined automated NOE assignment and structure calculation with CYANA","volume":"62","author":"G\u00fcntert","year":"2015","journal-title":"J. Biomol. NMR"},{"key":"2024050805420836300_B29","doi-asserted-by":"crossref","first-page":"1668","DOI":"10.1002\/jcc.20290","article-title":"The Amber biomolecular simulation programs","volume":"26","author":"Case","year":"2005","journal-title":"J. Comput. Chem."},{"key":"2024050805420836300_B30","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","article-title":"SciPy 1.0: fundamental algorithms for scientific computing in Python","volume":"17","author":"Virtanen","year":"2020","journal-title":"Nat. Methods"},{"key":"2024050805420836300_B31","doi-asserted-by":"crossref","first-page":"56","DOI":"10.25080\/Majora-92bf1922-00a","article-title":"Data structures for statistical computing in python","volume-title":"Proceedings of the 9th Python in Science Conference","author":"McKinney","year":"2010"},{"key":"2024050805420836300_B32","doi-asserted-by":"crossref","first-page":"1880","DOI":"10.1038\/s41467-024-46090-5","article-title":"Specificity, synergy, and mechanisms of splice-modifying drugs","volume":"15","author":"Ishigami","year":"2022","journal-title":"Nat. Commun."},{"key":"2024050805420836300_B33","doi-asserted-by":"crossref","first-page":"1150","DOI":"10.1038\/s41467-022-28653-6","article-title":"An orally available, brain penetrant, small molecule lowers huntingtin levels by enhancing pseudoexon inclusion","volume":"13","author":"Keller","year":"2022","journal-title":"Nat. Commun."},{"key":"2024050805420836300_B34","doi-asserted-by":"crossref","first-page":"D86","DOI":"10.1093\/nar\/gkq887","article-title":"DBASS3 and DBASS5: databases of aberrant 3\u2032- and 5\u2032-splice sites","volume":"39","author":"Buratti","year":"2011","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/advance-article-pdf\/doi\/10.1093\/nar\/gkae201\/57446177\/gkae201.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/advance-article-pdf\/doi\/10.1093\/nar\/gkae201\/57446177\/gkae201.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,8]],"date-time":"2024-05-08T05:42:45Z","timestamp":1715146965000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/52\/8\/4124\/7637893"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,30]]},"references-count":34,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2024,3,30]]},"published-print":{"date-parts":[[2024,5,8]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkae201","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,5,8]]},"published":{"date-parts":[[2024,3,30]]}}}