Structure-based discovery of small molecules that allosterically modulate RNA function

Structure-based discovery of small molecules that allosterically modulate RNA function | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Structure-based discovery of small molecules that allosterically modulate RNA function Zhaoming Su, Zhiling Pan, Hao Wu, Han Hu, Jian Zou, Haiyun Ma, and 10 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9338412/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract RNAs play essential roles in biological processes and have emerged as promising therapeutic targets for both oligonucleotide- and small molecule-based interventions. However, targeting RNAs with small molecules remain challenging due to our limited understandings of the chemical space associated with RNA-binding small molecules, the intricate three-dimensional RNA structures and ligand-binding pockets, and the molecular basis of small-molecule modes of action (MOAs). In this study, we discovered Hit Small molecules TArgeting RNA Structures (HitSTARS) through the following three stages. We first curated a library of 5.2 million in-stock Commercial Small molecules TArgeting RNA (CSTAR) through training a molecular representation learning model based on 3D atom positions, and explored their physicochemical properties. Next, virtual screening of CSTAR against the paradigmatic Tetrahymena ScaI L-16 ribozyme, as a proof of concept, identified two novel allosteric pockets. Functional screening of the top-scoring 125 compounds, validated by multiple docking algorithms, resulted in nine hit RNA-binders capable of inhibiting catalysis. Finally, cryo-EM structures of the best hit of each allosteric site, ZPT-005 and ZPT-084, in complexes with L-16 were determined at 2.3 Å and 3.0 Å resolutions to elucidate their modes of action: ZPT-005 stabilizes J1/2 in the undocked conformation upon binding to site 1, whereas ZPT-084 occupies site 2 to displace the catalytic core away from the splice site. These results facilitated lead optimization of ZPT-084 that improved the binding affinity and activity by 104- and 15-fold. Collectively, HitSTARS provides a comprehensive framework for streamlining RNA structure-based chemical probe discovery while offering insights into their MOAs. Biological sciences/Chemical biology Biological sciences/Structural biology Full Text Additional Declarations There is NO Competing Interest. Supplementary Files RiboBindv2.zip The code for the RiboBIND model trained to curate CSTAR library NstateZPT0059UTIvalreport.pdf PDB validation report of ZPT-005-bound L-16 in N state NstateZPT0849J9Xvalreport.pdf PDB validation report of ZPT-084-bound L-16 in N state Istate9JC8valreportfull.pdf PDB validation report of ZPT-084 induced L-16 I state SupplementaryData1.xlsx Positive and negative sets for model training and other sets used in SHAP analysis SIV3.pdf Supplementary figures and tables movieS1.mp4 MOA video of ZPT-084 inhibiting L-16 enzyme activity SupplementaryData2.xlsx Information of 125 purchased compounds machinelearningchecklist.pdf machine-learning-checklist NstateZPT0059UTI2.txt Atomic coordinate model of ZPT-005-bound L-16 in N state nrsoftwarepolicy.pdf nr-software-policy NstateZPT0849J9X.txt Atomic coordinate model of ZPT-084-bound L-16 in N state Istate9JC8.txt Atomic coordinate model of ZPT-084 induced L-16 I state nrreportingsummary.pdf nr-reporting-summary NstateZPT084EMD61283.mrc Cryo-EM map of of ZPT-084-bound L-16 in N state IstateEMD61359.mrc Cryo-EM map of of ZPT-084 induced L-16 I state NstateZPT005EMD64492.mrc Cryo-EM map of of ZPT-005-bound L-16 in N state Cite Share Download PDF Status: Under Review Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-9338412","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":624507170,"identity":"b306d67e-2a55-4e3d-88fa-0ff70780cc75","order_by":0,"name":"Zhaoming Su","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA7klEQVRIiWNgGAWjYHACxgOMDTY8bOzNB4AcCRmi9AC1pMnx8RxLAGnhIVbLYWM5iRwDEIewFvn+MwYHfu5gTmyTyPn86kaNBQ8D++GjG/BpYZyRY3Cw9wxbYhvP223WOceADuNJS7uBTwuzBI/BAd42nsQ29txtxjlsQC0SPGZ4tbDxnzE4+LdNIrGNIeeZcc4/IrTwMOQYHOZtMzBm48hhfpzbRoQWCYm0gsOyZxLk2HiOmTHn9knwsBHyi3z/4Y0P3+74zyPf3vz4c863Ojl+9sPH8GpB8ZcEmCRWOQgwfyBF9SgYBaNgFIwcAACa/0dv58sqegAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0002-9279-1721","institution":"West China Hospital","correspondingAuthor":true,"prefix":"","firstName":"Zhaoming","middleName":"","lastName":"Su","suffix":""},{"id":624507171,"identity":"c1579f1d-b11d-4080-a2ac-3f9ef167a9b5","order_by":1,"name":"Zhiling Pan","email":"","orcid":"","institution":"Chengdu university","correspondingAuthor":false,"prefix":"","firstName":"Zhiling","middleName":"","lastName":"Pan","suffix":""},{"id":624507172,"identity":"633fe53f-fcac-4059-bf23-5379a809e709","order_by":2,"name":"Hao Wu","email":"","orcid":"","institution":"Fudan University","correspondingAuthor":false,"prefix":"","firstName":"Hao","middleName":"","lastName":"Wu","suffix":""},{"id":624507173,"identity":"d30b36be-c50e-499b-8301-8b2bae08cc73","order_by":3,"name":"Han Hu","email":"","orcid":"","institution":"Mingle Scope","correspondingAuthor":false,"prefix":"","firstName":"Han","middleName":"","lastName":"Hu","suffix":""},{"id":624507174,"identity":"ec23db15-db19-4710-99d4-e6cfb49de76b","order_by":4,"name":"Jian Zou","email":"","orcid":"","institution":"Sichuan University","correspondingAuthor":false,"prefix":"","firstName":"Jian","middleName":"","lastName":"Zou","suffix":""},{"id":624507175,"identity":"10e67f32-7d22-49f7-bfb4-26f39c3bec7c","order_by":5,"name":"Haiyun Ma","email":"","orcid":"","institution":"Sichuan University","correspondingAuthor":false,"prefix":"","firstName":"Haiyun","middleName":"","lastName":"Ma","suffix":""},{"id":624507176,"identity":"19554bb1-e672-4feb-aa6e-6e62c32e9471","order_by":6,"name":"Hongshan Ni","email":"","orcid":"","institution":"Sichuan university","correspondingAuthor":false,"prefix":"","firstName":"Hongshan","middleName":"","lastName":"Ni","suffix":""},{"id":624507177,"identity":"c5201d6f-880f-45af-8c4f-a33dbda81d64","order_by":7,"name":"Liu Wang","email":"","orcid":"https://orcid.org/0000-0003-1243-9654","institution":"Sichuan University","correspondingAuthor":false,"prefix":"","firstName":"Liu","middleName":"","lastName":"Wang","suffix":""},{"id":624507178,"identity":"cd350740-6a37-43ba-aa01-a46cbc084655","order_by":8,"name":"Jiaqi Zhao","email":"","orcid":"","institution":"Mingle Scope","correspondingAuthor":false,"prefix":"","firstName":"Jiaqi","middleName":"","lastName":"Zhao","suffix":""},{"id":624507179,"identity":"fe43dace-0c6f-43ce-90b3-6b68ec23817d","order_by":9,"name":"Xiaoqi Sun","email":"","orcid":"","institution":"University of Chinese Academy of Sciences","correspondingAuthor":false,"prefix":"","firstName":"Xiaoqi","middleName":"","lastName":"Sun","suffix":""},{"id":624507180,"identity":"3f3b3220-ac43-406b-851d-683a01b8d903","order_by":10,"name":"Jiayu Dong","email":"","orcid":"","institution":"University of Chinese Academy of Sciences","correspondingAuthor":false,"prefix":"","firstName":"Jiayu","middleName":"","lastName":"Dong","suffix":""},{"id":624507181,"identity":"ec944317-c47b-4e22-897f-4b8b4727c102","order_by":11,"name":"Sheng Xu","email":"","orcid":"https://orcid.org/0000-0002-6507-9122","institution":"Fudan University","correspondingAuthor":false,"prefix":"","firstName":"Sheng","middleName":"","lastName":"Xu","suffix":""},{"id":624507182,"identity":"c40fa4fa-24e8-493a-a153-f2096824647c","order_by":12,"name":"Yu Cheng","email":"","orcid":"https://orcid.org/0000-0002-7901-8662","institution":"The Chinese University of Hong Kong","correspondingAuthor":false,"prefix":"","firstName":"Yu","middleName":"","lastName":"Cheng","suffix":""},{"id":624507183,"identity":"063f5a21-db34-4f89-96be-dfa256fd02a2","order_by":13,"name":"Ling Liu","email":"","orcid":"https://orcid.org/0000-0002-4882-0396","institution":"Institute of Microbiology, Chinese Academy of Sciences","correspondingAuthor":false,"prefix":"","firstName":"Ling","middleName":"","lastName":"Liu","suffix":""},{"id":624507184,"identity":"d1be76f8-482a-4222-8ea5-e3730a23ee69","order_by":14,"name":"Ke Zheng","email":"","orcid":"https://orcid.org/0000-0002-3345-7715","institution":"College of Chemistry, Sichuan University","correspondingAuthor":false,"prefix":"","firstName":"Ke","middleName":"","lastName":"Zheng","suffix":""},{"id":624507185,"identity":"80991307-1160-4da1-bc78-3b36d0edbf9e","order_by":15,"name":"Siqi Sun","email":"","orcid":"https://orcid.org/0000-0001-7240-8724","institution":"Fudan university","correspondingAuthor":false,"prefix":"","firstName":"Siqi","middleName":"","lastName":"Sun","suffix":""}],"badges":[],"createdAt":"2026-04-07 02:30:17","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-9338412/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-9338412/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":107488982,"identity":"dfafde7a-b99d-456c-b5f4-9056ad035060","added_by":"auto","created_at":"2026-04-22 02:46:19","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2880748,"visible":true,"origin":"","legend":"Article File","description":"","filename":"MaintextV420260416.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1_covered_55393879-a66d-415b-9aa7-fb33bdd854aa.pdf"},{"id":107282679,"identity":"c63aa6de-b803-49c3-a17b-ff858371ef21","added_by":"auto","created_at":"2026-04-20 02:46:33","extension":"zip","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":9437,"visible":true,"origin":"","legend":"The code for the RiboBIND model trained to curate CSTAR library","description":"","filename":"RiboBindv2.zip","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/96f53ae1bd827dd5b410d47e.zip"},{"id":107485486,"identity":"59f33f87-49f5-4aef-941f-9a11be36980a","added_by":"auto","created_at":"2026-04-22 02:35:10","extension":"pdf","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":1393961,"visible":true,"origin":"","legend":"PDB validation report of ZPT-005-bound L-16 in N state","description":"","filename":"NstateZPT0059UTIvalreport.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/557f203ee783a037897e9241.pdf"},{"id":107485488,"identity":"73b3ab4b-8f67-4cc6-9a70-9cbd001e25a0","added_by":"auto","created_at":"2026-04-22 02:35:10","extension":"pdf","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":1823779,"visible":true,"origin":"","legend":"PDB validation report of ZPT-084-bound L-16 in N state","description":"","filename":"NstateZPT0849J9Xvalreport.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/db39ea55cf5a42d90c4d3bb8.pdf"},{"id":107282681,"identity":"bcd21e99-396b-48b6-9120-95db35592709","added_by":"auto","created_at":"2026-04-20 02:46:33","extension":"pdf","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":1403870,"visible":true,"origin":"","legend":"PDB validation report of ZPT-084 induced L-16 I state","description":"","filename":"Istate9JC8valreportfull.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/752f8f2b1fc02860a12c0b7a.pdf"},{"id":107485494,"identity":"4c849f03-69d0-43c9-b079-30008f3c44cd","added_by":"auto","created_at":"2026-04-22 02:35:11","extension":"xlsx","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":832732,"visible":true,"origin":"","legend":"Positive and negative sets for model training and other sets used in SHAP analysis","description":"","filename":"SupplementaryData1.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/0a612d12b3be207b6f6cc558.xlsx"},{"id":107486584,"identity":"444d4017-6f69-4c90-983a-6c6cb9dc550a","added_by":"auto","created_at":"2026-04-22 02:38:24","extension":"pdf","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":16473261,"visible":true,"origin":"","legend":"Supplementary figures and tables","description":"","filename":"SIV3.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/fa7803e31d38b1bb2c4fb5c9.pdf"},{"id":107282683,"identity":"1c64c424-f3d3-47f8-9789-baf820016b98","added_by":"auto","created_at":"2026-04-20 02:46:33","extension":"mp4","order_by":7,"title":"","display":"","copyAsset":false,"role":"supplement","size":44173639,"visible":true,"origin":"","legend":"MOA video of ZPT-084 inhibiting L-16 enzyme activity","description":"","filename":"movieS1.mp4","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/e3ede002c2d5b74c750223e9.mp4"},{"id":107484224,"identity":"d2185ed0-f7b0-4a0d-be71-13c624a6baf0","added_by":"auto","created_at":"2026-04-22 02:31:10","extension":"xlsx","order_by":8,"title":"","display":"","copyAsset":false,"role":"supplement","size":24610,"visible":true,"origin":"","legend":"Information of 125 purchased compounds","description":"","filename":"SupplementaryData2.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/89eeba5980655a3cb053b01d.xlsx"},{"id":107282685,"identity":"059863f7-9562-4726-8280-9b3ca8feb8c8","added_by":"auto","created_at":"2026-04-20 02:46:33","extension":"pdf","order_by":9,"title":"","display":"","copyAsset":false,"role":"supplement","size":303329,"visible":true,"origin":"","legend":"machine-learning-checklist","description":"","filename":"machinelearningchecklist.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/3f532d05a257aa8c5009b981.pdf"},{"id":107483448,"identity":"98aea43a-1676-4b35-ae4f-06f90d37ec66","added_by":"auto","created_at":"2026-04-22 02:27:47","extension":"txt","order_by":10,"title":"","display":"","copyAsset":false,"role":"supplement","size":705190,"visible":true,"origin":"","legend":"Atomic coordinate model of ZPT-005-bound L-16 in N state","description":"","filename":"NstateZPT0059UTI2.txt","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/5318e3c32fb04a3c4bb7a850.txt"},{"id":107483451,"identity":"af89bce7-6e3a-408a-8889-4dddfbfdbaef","added_by":"auto","created_at":"2026-04-22 02:27:48","extension":"pdf","order_by":11,"title":"","display":"","copyAsset":false,"role":"supplement","size":1317086,"visible":true,"origin":"","legend":"nr-software-policy","description":"","filename":"nrsoftwarepolicy.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/c96698db4fe3eefc68d77b45.pdf"},{"id":107282688,"identity":"627fa74b-ba99-49fe-8fa2-f249a43fe179","added_by":"auto","created_at":"2026-04-20 02:46:33","extension":"txt","order_by":12,"title":"","display":"","copyAsset":false,"role":"supplement","size":652750,"visible":true,"origin":"","legend":"Atomic coordinate model of ZPT-084-bound L-16 in N state","description":"","filename":"NstateZPT0849J9X.txt","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/b367f76ab9f2de73b1ff1cf6.txt"},{"id":107484105,"identity":"a75d6a95-77e7-4d83-b4e2-abcb2f4e3a9e","added_by":"auto","created_at":"2026-04-22 02:30:46","extension":"txt","order_by":13,"title":"","display":"","copyAsset":false,"role":"supplement","size":658630,"visible":true,"origin":"","legend":"Atomic coordinate model of ZPT-084 induced L-16 I state","description":"","filename":"Istate9JC8.txt","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/3ce2f795215d66305232338a.txt"},{"id":107282693,"identity":"f342cb36-4a79-472f-b906-f4fa1a1d11ac","added_by":"auto","created_at":"2026-04-20 02:46:33","extension":"pdf","order_by":14,"title":"","display":"","copyAsset":false,"role":"supplement","size":1665617,"visible":true,"origin":"","legend":"nr-reporting-summary","description":"","filename":"nrreportingsummary.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/4cb3a4bf088a899f146f73f9.pdf"},{"id":107282694,"identity":"19e067a4-7a55-491a-810b-7953094a4ff5","added_by":"auto","created_at":"2026-04-20 02:46:33","extension":"mrc","order_by":15,"title":"","display":"","copyAsset":false,"role":"supplement","size":44958720,"visible":true,"origin":"","legend":"Cryo-EM map of of ZPT-084-bound L-16 in N state","description":"","filename":"NstateZPT084EMD61283.mrc","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/b20f19527b51a530bd97df1a.mrc"},{"id":107282691,"identity":"3ca01605-7c96-45c6-878a-13f55cf77b7b","added_by":"auto","created_at":"2026-04-20 02:46:33","extension":"mrc","order_by":16,"title":"","display":"","copyAsset":false,"role":"supplement","size":67109888,"visible":true,"origin":"","legend":"Cryo-EM map of of ZPT-084 induced L-16 I state","description":"","filename":"IstateEMD61359.mrc","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/fff494bcca761e3719e0cbc2.mrc"},{"id":107483668,"identity":"9ecfbf05-d745-4c21-a272-15b86288470c","added_by":"auto","created_at":"2026-04-22 02:28:41","extension":"mrc","order_by":17,"title":"","display":"","copyAsset":false,"role":"supplement","size":108001024,"visible":true,"origin":"","legend":"Cryo-EM map of of ZPT-005-bound L-16 in N state","description":"","filename":"NstateZPT005EMD64492.mrc","url":"https://assets-eu.researchsquare.com/files/rs-9338412/v1/d6091cb649ab54fb71eb9fe1.mrc"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"Structure-based discovery of small molecules that allosterically modulate RNA function","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-9338412/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-9338412/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"RNAs play essential roles in biological processes and have emerged as promising therapeutic targets for both oligonucleotide- and small molecule-based interventions. However, targeting RNAs with small molecules remain challenging due to our limited understandings of the chemical space associated with RNA-binding small molecules, the intricate three-dimensional RNA structures and ligand-binding pockets, and the molecular basis of small-molecule modes of action (MOAs). In this study, we discovered Hit Small molecules TArgeting RNA Structures (HitSTARS) through the following three stages. We first curated a library of 5.2 million in-stock Commercial Small molecules TArgeting RNA (CSTAR) through training a molecular representation learning model based on 3D atom positions, and explored their physicochemical properties. Next, virtual screening of CSTAR against the paradigmatic Tetrahymena ScaI L-16 ribozyme, as a proof of concept, identified two novel allosteric pockets. Functional screening of the top-scoring 125 compounds, validated by multiple docking algorithms, resulted in nine hit RNA-binders capable of inhibiting catalysis. Finally, cryo-EM structures of the best hit of each allosteric site, ZPT-005 and ZPT-084, in complexes with L-16 were determined at 2.3 Å and 3.0 Å resolutions to elucidate their modes of action: ZPT-005 stabilizes J1/2 in the undocked conformation upon binding to site 1, whereas ZPT-084 occupies site 2 to displace the catalytic core away from the splice site. These results facilitated lead optimization of ZPT-084 that improved the binding affinity and activity by 104- and 15-fold. Collectively, HitSTARS provides a comprehensive framework for streamlining RNA structure-based chemical probe discovery while offering insights into their MOAs.","manuscriptTitle":"Structure-based discovery of small molecules that allosterically modulate RNA function","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-04-20 02:46:23","doi":"10.21203/rs.3.rs-9338412/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"nature-communications","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"NCOMMS","sideBox":"Learn more about [Nature Communications](http://www.nature.com/ncomms/)","snPcode":"","submissionUrl":"https://mts-ncomms.nature.com/","title":"Nature Communications","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature Communications","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"18400853-6d3d-42f5-812b-b94da9e474ef","owner":[],"postedDate":"April 20th, 2026","published":true,"recentEditorialEvents":[{"type":"reviewerAgreed","content":"This content is not available.","date":"2026-05-12T10:20:57+00:00","index":3,"fulltext":"This content is not available."},{"type":"editorInvitedReview","content":"This content is not available.","date":"2026-05-06T00:41:19+00:00","index":1,"fulltext":"This content is not available."},{"type":"editorInvitedReview","content":"This content is not available.","date":"2026-05-04T02:37:33+00:00","index":2,"fulltext":"This content is not available."}],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":66471682,"name":"Biological sciences/Chemical biology"},{"id":66471683,"name":"Biological sciences/Structural biology"}],"tags":[],"updatedAt":"2026-04-20T02:46:23+00:00","versionOfRecord":[],"versionCreatedAt":"2026-04-20 02:46:23","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-9338412","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-9338412","identity":"rs-9338412","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}