Structure-Based Drug Repurposing Reveals State-Independent Binding of MCC950 to the NLRP3 Inflammasome: Implications for Alzheimer’s Disease

Structure-Based Drug Repurposing Reveals State-Independent Binding of MCC950 to the NLRP3 Inflammasome: Implications for Alzheimer’s Disease | 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 Research Article Structure-Based Drug Repurposing Reveals State-Independent Binding of MCC950 to the NLRP3 Inflammasome: Implications for Alzheimer’s Disease Siddarth Raajasekar, Madhumitra Thangadurai, Sathish Kumar Marimuthu This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9251932/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background Alzheimer disease (AD) is extensively accepted as a chronic neuroinflammatory disease, and the NLRP3 inflammasome is one of the critical factor in the pathogenesis of the disease. Neuroprotective activity in preclinical models of AD has been shown with MCC950, a potent small molecule NLRP3 inhibitor. Nevertheless, the molecular mechanism of NLRP3 repression is not fully elucidated, especially since the protein displays a significant conformational flexibility in the activation process. The typical structure based drugs discovery paradigm that employs the single protein conformation might not reproduce the dynamic properties of the protein ligand interaction. Methods We employed a multi-structure molecular docking technique to evaluate binding characteristics of three known NLRP3 inhibitors MCC950, oridonin, and parthenolide across four experimentally resolved human NLRP3 structures (PDB: 6NPY, 7PZC, 8SXN, 9GU4) representing inactive, intermediate, and active conformational states. Binding affinity, interaction networks (hydrogen bonds, hydrophobic contacts, π-π stacking), pose stability (RMSD analysis), and binding depth were sequentially compared across conformations using AutoDock Vina, PLIP, and PyMOL. Results MCC950 exhibited strong state independent binding with a uniformly high affinity (mean docking score: -9.3 ± 0.2 kcal/mol), conserved hydrogen bonding binding with ARG167 and TYR381, and comprehensive hydrophobicity as well as remarkably low pose variability in all the conformations. On the contadictory, the interaction between oridonin and parthenolide was conformation reliant with reduced strength, with inconsistent patterns of interaction and possessing greater pose instability (mean RMSD: 3.1 and 4.1 A, respectively). MC950 was very ingrained in the NACHT domain pocket (76–80% buried), but natural compounds were attached more marginally. Conclusions MCC950 displays a better conformational stability than natural NLRP3 inhibitors and it can bind to a diversity of protein states in a stable manner. This binding property is independent of the state and act as a molecular explanation of MCC950 and its stable efficacy in preclinical investigations and its therapeutic potential in AD and other neuroinflammatory disorders. The multi structure docking method offers a more realistic structure grounded approach to drug discovery of conformationally dynamic proteins. Bioinformatics NLRP3 inflammasome Alzheimer’s disease MCC950 molecular docking neuroinflammation drug repurposing state-independent binding conformational dynamics Full Text Additional Declarations The authors declare no competing interests. Cite Share Download PDF Status: Posted 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-9251932","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":613711792,"identity":"f96f147d-f3d0-42ff-a8b5-6edbe2d23c41","order_by":0,"name":"Siddarth Raajasekar","email":"data:image/png;base64,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","orcid":"https://orcid.org/0000-0002-1361-0815","institution":"KIT-KalaignarKarunanidhi Institute of Technology","correspondingAuthor":true,"prefix":"","firstName":"Siddarth","middleName":"","lastName":"Raajasekar","suffix":""},{"id":613711793,"identity":"35a427b0-b2de-4628-b4d4-3f296ff34caf","order_by":1,"name":"Madhumitra Thangadurai","email":"","orcid":"","institution":"SASTRA Deemed University","correspondingAuthor":false,"prefix":"","firstName":"Madhumitra","middleName":"","lastName":"Thangadurai","suffix":""},{"id":613711794,"identity":"332624c2-41fd-4764-8792-49378cca858f","order_by":2,"name":"Sathish Kumar Marimuthu","email":"","orcid":"","institution":"KIRND Institute of Research \u0026 Development","correspondingAuthor":false,"prefix":"","firstName":"Sathish","middleName":"Kumar","lastName":"Marimuthu","suffix":""}],"badges":[],"createdAt":"2026-03-28 10:34:40","currentVersionCode":1,"declarations":{"humanSubjects":false,"vertebrateSubjects":false,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":false},"doi":"10.21203/rs.3.rs-9251932/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-9251932/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":105904111,"identity":"5f9366bb-c70b-4d21-ba73-e3f0629bf57b","added_by":"auto","created_at":"2026-04-01 10:04:25","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2486424,"visible":true,"origin":"","legend":"","description":"","filename":"MCC950repurposing.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9251932/v1_covered_78817d2a-785b-41bf-8c3a-e383c298533c.pdf"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003eStructure-Based Drug Repurposing Reveals State-Independent Binding of MCC950 to the NLRP3 Inflammasome: Implications for Alzheimer’s Disease\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"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":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"NLRP3 inflammasome, Alzheimer’s disease, MCC950, molecular docking, neuroinflammation, drug repurposing, state-independent binding, conformational dynamics","lastPublishedDoi":"10.21203/rs.3.rs-9251932/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-9251932/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e \u003cp\u003eAlzheimer disease (AD) is extensively accepted as a chronic neuroinflammatory disease, and the NLRP3 inflammasome is one of the critical factor in the pathogenesis of the disease. Neuroprotective activity in preclinical models of AD has been shown with MCC950, a potent small molecule NLRP3 inhibitor. Nevertheless, the molecular mechanism of NLRP3 repression is not fully elucidated, especially since the protein displays a significant conformational flexibility in the activation process. The typical structure based drugs discovery paradigm that employs the single protein conformation might not reproduce the dynamic properties of the protein ligand interaction.\u003c/p\u003e\u003ch2\u003eMethods\u003c/h2\u003e \u003cp\u003eWe employed a multi-structure molecular docking technique to evaluate binding characteristics of three known NLRP3 inhibitors MCC950, oridonin, and parthenolide across four experimentally resolved human NLRP3 structures (PDB: 6NPY, 7PZC, 8SXN, 9GU4) representing inactive, intermediate, and active conformational states. Binding affinity, interaction networks (hydrogen bonds, hydrophobic contacts, π-π stacking), pose stability (RMSD analysis), and binding depth were sequentially compared across conformations using AutoDock Vina, PLIP, and PyMOL.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003eMCC950 exhibited strong state independent binding with a uniformly high affinity (mean docking score: -9.3\u0026thinsp;\u0026plusmn;\u0026thinsp;0.2 kcal/mol), conserved hydrogen bonding binding with ARG167 and TYR381, and comprehensive hydrophobicity as well as remarkably low pose variability in all the conformations. On the contadictory, the interaction between oridonin and parthenolide was conformation reliant with reduced strength, with inconsistent patterns of interaction and possessing greater pose instability (mean RMSD: 3.1 and 4.1 A, respectively). MC950 was very ingrained in the NACHT domain pocket (76\u0026ndash;80% buried), but natural compounds were attached more marginally.\u003c/p\u003e\u003ch2\u003eConclusions\u003c/h2\u003e \u003cp\u003eMCC950 displays a better conformational stability than natural NLRP3 inhibitors and it can bind to a diversity of protein states in a stable manner. This binding property is independent of the state and act as a molecular explanation of MCC950 and its stable efficacy in preclinical investigations and its therapeutic potential in AD and other neuroinflammatory disorders. The multi structure docking method offers a more realistic structure grounded approach to drug discovery of conformationally dynamic proteins.\u003c/p\u003e","manuscriptTitle":"Structure-Based Drug Repurposing Reveals State-Independent Binding of MCC950 to the NLRP3 Inflammasome: Implications for Alzheimer’s Disease","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-03-31 04:52:31","doi":"10.21203/rs.3.rs-9251932/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"402cd91a-9a05-41be-9e44-294b991c5ad2","owner":[],"postedDate":"March 31st, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":65306033,"name":"Bioinformatics"}],"tags":[],"updatedAt":"2026-03-31T04:52:31+00:00","versionOfRecord":[],"versionCreatedAt":"2026-03-31 04:52:31","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-9251932","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-9251932","identity":"rs-9251932","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}