Elucidating the Molecular Binding Mechanism of Banxia Xiexin Decoction Components with Acute Gastroenteritis Targets: An Integrated Approach Combining Network Pharmacology and 100-ns Molecular Dynamics Simulations

Elucidating the Molecular Binding Mechanism of Banxia Xiexin Decoction Components with Acute Gastroenteritis Targets: An Integrated Approach Combining Network Pharmacology and 100-ns Molecular Dynamics Simulations | 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 Elucidating the Molecular Binding Mechanism of Banxia Xiexin Decoction Components with Acute Gastroenteritis Targets: An Integrated Approach Combining Network Pharmacology and 100-ns Molecular Dynamics Simulations Tao Li, Yuan Chen, Ying Qian Zhou, Li xin Du, Long Zou This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8924942/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 Objective: This study aimed to elucidate the molecular binding mechanism and structural stability of the active components of Banxia Xiexin Decoction (BXD) against core therapeutic targets of acute gastroenteritis (AGE) using an integrated computational framework. Methods: Active chemical constituents and AGE-related targets were retrieved from public databases (TCMSP, SwissTargetPrediction, GeneCards). Following the construction of a protein–protein interaction (PPI) network to identify core targets, molecular docking was performed to screen key active compounds. Crucially, to validate the thermodynamic stability of ligand-target interactions, 100-ns molecular dynamics (MD) simulations were conducted using GROMACS. MM-PBSA free energy calculations and Free Energy Landscape (FEL) analyses were subsequently performed to quantify binding energetics and conformational stability. Results: Network analysis identified TNF and STAT3 as core targets regulated by BXD. Molecular docking revealed that isorhamnetin and 7-methoxy-2-methyl-isoflavone exhibit strong binding affinities (-8.4 and -8.7 kcal/mol, respectively) to these targets. MD simulations confirmed that the ligand-protein complexes maintained stable conformations with minimal RMSD fluctuations. Notably, MM-PBSA decomposition demonstrated a robust binding free energy of -133.97 ± 12.83 kJ/mol for the TNF–isorhamnetin complex, driven primarily by van der Waals and electrostatic interactions. FEL analysis further verified that the complexes reside in stable low-energy basins. Conclusion: The integrated analyses provide a solid structural and thermodynamic basis for BXD’s anti-inflammatory effects in AGE. The results suggest that key BXD components can stably occupy the active sites of TNF and STAT3, potentially disrupting pathological signaling loops, which warrants future experimental exploration. Banxia Xiexin Decoction (BXD) acute gastroenteritis(AGE) network pharmacology molecular docking molecular dynamics simulation MM-PBSA Full Text Additional Declarations No competing interests reported. Author Contributions Tao Li: Investigation, Data curation, Formal analysis, Writing – Original draft Yuan Chen: Methodology, Validation Yingqian Zhou: Visualization, Software Lixin Du: Resources, Project administration Long Zou: Conceptualization, Supervision, Writing – Review & Editing All authors have read and approved the final manuscript. Supplementary Files Checklist.docx Highlights.docx STAT37Methoxy2methylisoflavone90100ns.mp4 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. 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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-8924942","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":600130276,"identity":"c86fed16-5fa7-4709-bfb8-64a820201cb7","order_by":0,"name":"Tao Li","email":"","orcid":"","institution":"Hunan University of Chinese Medicine","correspondingAuthor":false,"prefix":"","firstName":"Tao","middleName":"","lastName":"Li","suffix":""},{"id":600130277,"identity":"08e08d60-0f55-489a-9b9b-7de0762ce694","order_by":1,"name":"Yuan Chen","email":"","orcid":"","institution":"Hunan University of Chinese Medicine","correspondingAuthor":false,"prefix":"","firstName":"Yuan","middleName":"","lastName":"Chen","suffix":""},{"id":600130278,"identity":"898e2003-5b0c-434e-8e65-5d28457fc4bd","order_by":2,"name":"Ying Qian Zhou","email":"","orcid":"","institution":"Hunan University of Chinese Medicine","correspondingAuthor":false,"prefix":"","firstName":"Ying","middleName":"Qian","lastName":"Zhou","suffix":""},{"id":600130279,"identity":"82564460-bcda-44e0-8504-a0611186a61c","order_by":3,"name":"Li xin Du","email":"","orcid":"","institution":"Hunan University of Chinese Medicine","correspondingAuthor":false,"prefix":"","firstName":"Li","middleName":"xin","lastName":"Du","suffix":""},{"id":600130280,"identity":"3033f172-aef9-43a7-8dd9-303db573d518","order_by":4,"name":"Long Zou","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA0UlEQVRIie3QMQuCQBTA8QtBGwRXHfoODwQjjD7LHYIuIkJLQ8NNTkKrH8OPcHJQi9V64JzzQWtEBi4NaW4N998evN8bHkIq1R+maxpjEta4n7VxYhkZqYo0nECcvHb5XPIJBAQGjuCaLO3gVqKdT6hxZmME8xSa7aoIPYHqiFAzwWOE8QIaUopYF7OME2qbMEII5SZcevL8gTg5Rx1hPaE/kO7JqCogIGXdegIfIzcz42Gia9ZdyseGlKegFXLvLw5GPUw+w+8jE/ZVKpVK9aUXmkRQV78kZacAAAAASUVORK5CYII=","orcid":"","institution":"Hunan University of Chinese Medicine","correspondingAuthor":true,"prefix":"","firstName":"Long","middleName":"","lastName":"Zou","suffix":""}],"badges":[],"createdAt":"2026-02-20 10:57:39","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8924942/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8924942/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":105724706,"identity":"70faa2ab-6263-40f0-99d2-9e9e16c72e83","added_by":"auto","created_at":"2026-03-30 10:13:44","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2103973,"visible":true,"origin":"","legend":"","description":"","filename":"Manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8924942/v1_covered_cad9daa8-2898-4a02-ba3f-adc7528a937c.pdf"},{"id":103947314,"identity":"36687ce9-476e-4b07-8d93-e6c1c014f2b6","added_by":"auto","created_at":"2026-03-04 22:32:54","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":13751,"visible":true,"origin":"","legend":"","description":"","filename":"Checklist.docx","url":"https://assets-eu.researchsquare.com/files/rs-8924942/v1/521b14cd789e0d234689673b.docx"},{"id":103947313,"identity":"2849e0f5-a337-4166-a892-2c3b794c7a36","added_by":"auto","created_at":"2026-03-04 22:32:54","extension":"docx","order_by":7,"title":"","display":"","copyAsset":false,"role":"supplement","size":15019,"visible":true,"origin":"","legend":"","description":"","filename":"Highlights.docx","url":"https://assets-eu.researchsquare.com/files/rs-8924942/v1/0b29e9488305b21f2b6f93e2.docx"},{"id":103947315,"identity":"d4ab7ee5-2ea7-4612-9f66-4a3a54a4a4d8","added_by":"auto","created_at":"2026-03-04 22:32:54","extension":"mp4","order_by":8,"title":"","display":"","copyAsset":false,"role":"supplement","size":5830260,"visible":true,"origin":"","legend":"","description":"","filename":"STAT37Methoxy2methylisoflavone90100ns.mp4","url":"https://assets-eu.researchsquare.com/files/rs-8924942/v1/8c7d75d565a87b23fb2609f2.mp4"}],"financialInterests":"\u003cp\u003eNo competing interests reported.\u003c/p\u003e\n\u003cp\u003eAuthor Contributions\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTao Li:\u003c/strong\u003e Investigation, Data curation, Formal analysis, Writing – Original draft\u003cbr\u003e\n\u003cstrong\u003eYuan Chen:\u003c/strong\u003e Methodology, Validation\u003cbr\u003e\n\u003cstrong\u003eYingqian Zhou:\u003c/strong\u003e Visualization, Software\u003cbr\u003e\n\u003cstrong\u003eLixin Du:\u003c/strong\u003e Resources, Project administration\u003cbr\u003e\n\u003cstrong\u003eLong Zou:\u003c/strong\u003e Conceptualization, Supervision, Writing – Review \u0026amp; Editing\u003c/p\u003e\n\u003cp\u003eAll authors have read and approved the final manuscript.\u003c/p\u003e","formattedTitle":"Elucidating the Molecular Binding Mechanism of Banxia Xiexin Decoction Components with Acute Gastroenteritis Targets: An Integrated Approach Combining Network Pharmacology and 100-ns Molecular Dynamics Simulations","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":"Banxia Xiexin Decoction (BXD), acute gastroenteritis(AGE), network pharmacology, molecular docking, molecular dynamics simulation, MM-PBSA","lastPublishedDoi":"10.21203/rs.3.rs-8924942/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8924942/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eObjective:\u003c/p\u003e\n\u003cp\u003eThis study aimed to elucidate the molecular binding mechanism and structural stability of the active components of Banxia Xiexin Decoction (BXD) against core therapeutic targets of acute gastroenteritis (AGE) using an integrated computational framework.\u003c/p\u003e\n\u003cp\u003eMethods:\u003c/p\u003e\n\u003cp\u003eActive chemical constituents and AGE-related targets were retrieved from public databases (TCMSP, SwissTargetPrediction, GeneCards). Following the construction of a protein–protein interaction (PPI) network to identify core targets, molecular docking was performed to screen key active compounds. Crucially, to validate the thermodynamic stability of ligand-target interactions, 100-ns molecular dynamics (MD) simulations were conducted using GROMACS. MM-PBSA free energy calculations and Free Energy Landscape (FEL) analyses were subsequently performed to quantify binding energetics and conformational stability.\u003c/p\u003e\n\u003cp\u003eResults:\u003c/p\u003e\n\u003cp\u003eNetwork analysis identified TNF and STAT3 as core targets regulated by BXD. Molecular docking revealed that isorhamnetin and 7-methoxy-2-methyl-isoflavone exhibit strong binding affinities (-8.4 and -8.7 kcal/mol, respectively) to these targets. MD simulations confirmed that the ligand-protein complexes maintained stable conformations with minimal RMSD fluctuations. 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The results suggest that key BXD components can stably occupy the active sites of TNF and STAT3, potentially disrupting pathological signaling loops, which warrants future experimental exploration.\u003c/p\u003e","manuscriptTitle":"Elucidating the Molecular Binding Mechanism of Banxia Xiexin Decoction Components with Acute Gastroenteritis Targets: An Integrated Approach Combining Network Pharmacology and 100-ns Molecular Dynamics Simulations","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-03-04 22:32:49","doi":"10.21203/rs.3.rs-8924942/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":"0d904cf9-488d-4c73-a2b8-46e973e0c43b","owner":[],"postedDate":"March 4th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2026-03-30T10:12:29+00:00","versionOfRecord":[],"versionCreatedAt":"2026-03-04 22:32:49","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8924942","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8924942","identity":"rs-8924942","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}