TCoCPIn: Unveiling Topological Characteristics of Chemical-Protein Interaction Networks for Discovering Novel Features in Interactions

TCoCPIn: Unveiling Topological Characteristics of Chemical-Protein Interaction Networks for Discovering Novel Features in Interactions | 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 TCoCPIn: Unveiling Topological Characteristics of Chemical-Protein Interaction Networks for Discovering Novel Features in Interactions Jianshi WANG, Yukio OHSAWA This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4635465/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 The complexity of drug mechanisms of action, disease pathology, and protein function stems from the intricacies of chemical-protein interaction (CPI) networks. However, the lack of innovative analytical methods has hindered our ability to decipher the organization and function of CPI networks. To this end, we propose a new method, TCoCPIn, to reveal hidden patterns and relationships in CPI networks by applying topological features. By combining network topology with CPI data, TCoCPIn is able to discover new features in interactions, thereby facilitating the development of innovative therapeutic strategies. Through comprehensive analysis of specific datasets, we demonstrate the effectiveness of TCoCPIn in revealing small-world properties, key nodes, and communities in CPI networks, which may be associated with drug efficacy or toxicity. Our pioneering approach highlights the potential of topological analysis to elucidate the organization and function of CPI networks, thereby advancing drug discovery and improving our understanding of disease mechanisms. CPIs Network Topology Topological features Hidden Associations Full Text Additional Declarations No competing interests reported. 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-4635465","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":327681645,"identity":"da71a8e9-2793-4c6a-b01c-98bbc1b975bc","order_by":0,"name":"Jianshi WANG","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABEklEQVRIiWNgGAWjYBACxmYQ0SAB5hz8UGEjB2IceECkFsbHEmfSjMFaEgha1QCmmA142w4ngtn4tDC3Mz97+HOHRWL/7PZrEhJsh9Pnhx1+CLTFTk63AZfD2MyNec9IJM64c6ZMooAnPXfj7TQDoJZkY7MDOP1iJs3YJpHbcCMnTUJCwjp34+wEkJYDidtwamH/JvkTqGU+SAuPAXO64ez0DwS08JhJ8AK1bLiRftiAJ8E5QV46h5AtPGXSQC31G2/kAAP5QJrhBumcggMJBrj9Yth/fBvQYXXGcjfSHxz8+M9GXn52+uYPHyrs5HBqaYAzeQzAlAFYpQF25SAgj2CyP4CINGBRNgpGwSgYBSMaAAC95mU4ovKrUQAAAABJRU5ErkJggg==","orcid":"","institution":"The University of Tokyo","correspondingAuthor":true,"prefix":"","firstName":"Jianshi","middleName":"","lastName":"WANG","suffix":""},{"id":327681646,"identity":"cc04723c-773a-4b3d-83c6-01065a2b9546","order_by":1,"name":"Yukio OHSAWA","email":"","orcid":"","institution":"The University of Tokyo","correspondingAuthor":false,"prefix":"","firstName":"Yukio","middleName":"","lastName":"OHSAWA","suffix":""}],"badges":[],"createdAt":"2024-06-25 09:59:18","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4635465/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4635465/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":62274486,"identity":"7ee7d325-a6f8-445d-b5c4-0f2d6ea18448","added_by":"auto","created_at":"2024-08-12 10:59:06","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1024386,"visible":true,"origin":"","legend":"","description":"","filename":"TCoCPIn.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4635465/v1_covered_2611ec16-f5bb-4be4-b28a-d082f03136a6.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"TCoCPIn: Unveiling Topological Characteristics of Chemical-Protein Interaction Networks for Discovering Novel Features in Interactions","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"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":"CPIs, Network Topology,Topological features, Hidden Associations","lastPublishedDoi":"10.21203/rs.3.rs-4635465/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4635465/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"The complexity of drug mechanisms of action, disease pathology, and protein function stems from the intricacies of chemical-protein interaction (CPI) networks. 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