{"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":1792467171401,"version":"4.5.0"},"reference-count":58,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2021,7,20]],"date-time":"2021-07-20T00:00:00Z","timestamp":1626739200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"J. R. & Inez Jay Fund"},{"name":"University of Kansas General Research Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Risdiplam is the first approved small-molecule splicing modulator for the treatment of spinal muscular atrophy (SMA). Previous studies demonstrated that risdiplam analogues have two separate binding sites in exon 7 of the SMN2 pre-mRNA: (i) the 5\u2032-splice site and (ii) an upstream purine (GA)-rich binding site. Importantly, the sequence of this GA-rich binding site significantly enhanced the potency of risdiplam analogues. In this report, we unambiguously determined that a known risdiplam analogue, SMN-C2, binds to single-stranded GA-rich RNA in a sequence-specific manner. The minimum required binding sequence for SMN-C2 was identified as GAAGGAAGG. We performed all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method, which captured spontaneous binding of a risdiplam analogue to the target nucleic acids. We uncovered, for the first time, a ligand-binding pocket formed by two sequential GAAG loop-like structures. The simulation findings were highly consistent with experimental data obtained from saturation transfer difference (STD) NMR and structure-affinity-relationship studies of the risdiplam analogues. Together, these studies illuminate us to understand the molecular basis of single-stranded purine-rich RNA recognition by small-molecule splicing modulators with an unprecedented binding mode.<\/jats:p>","DOI":"10.1093\/nar\/gkab602","type":"journal-article","created":{"date-parts":[[2021,7,1]],"date-time":"2021-07-01T15:50:13Z","timestamp":1625154613000},"page":"7870-7883","source":"Crossref","is-referenced-by-count":38,"title":["Recognition of single-stranded nucleic acids by small-molecule splicing modulators"],"prefix":"10.1093","volume":"49","author":[{"given":"Zhichao","family":"Tang","sequence":"first","affiliation":[{"name":"Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sana","family":"Akhter","sequence":"additional","affiliation":[{"name":"Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ankita","family":"Ramprasad","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao","family":"Wang","sequence":"additional","affiliation":[{"name":"Analytical Research & Development, Merck and Co., Inc., Kenilworth, NJ 07033, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mikhail","family":"Reibarkh","sequence":"additional","affiliation":[{"name":"Analytical Research & Development, Merck and Co., Inc., Kenilworth, NJ 07033, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinan","family":"Wang","sequence":"additional","affiliation":[{"name":"Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sadikshya","family":"Aryal","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Srinivas S","family":"Thota","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junxing","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justin T","family":"Douglas","sequence":"additional","affiliation":[{"name":"Nuclear Magnetic Resonance Lab, University of Kansas, Lawrence, KS 66045, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip","family":"Gao","sequence":"additional","affiliation":[{"name":"Protein Production Group, University of Kansas, Lawrence, KS 66047, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2624-0806","authenticated-orcid":false,"given":"Erik D","family":"Holmstrom","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences and Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yinglong","family":"Miao","sequence":"additional","affiliation":[{"name":"Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9414-4093","authenticated-orcid":false,"given":"Jingxin","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,7,20]]},"reference":[{"key":"2021081818125443000_B1","doi-asserted-by":"crossref","first-page":"2120","DOI":"10.1016\/S0140-6736(08)60921-6","article-title":"Spinal muscular atrophy","volume":"371","author":"Lunn","year":"2008","journal-title":"Lancet"},{"key":"2021081818125443000_B2","doi-asserted-by":"crossref","first-page":"R111","DOI":"10.1093\/hmg\/ddq147","article-title":"Spinal muscular atrophy: mechanisms and therapeutic strategies","volume":"19","author":"Lorson","year":"2010","journal-title":"Hum. 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