Breaking Glycolysis: Allosteric Hotspots for Multi-Target Drug Repurposing

Breaking Glycolysis: Allosteric Hotspots for Multi-Target Drug Repurposing | 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 Breaking Glycolysis: Allosteric Hotspots for Multi-Target Drug Repurposing Latife Sude Vural, Elcin Kahraman, Simay Mintemur, Sinem Urhan, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9149499/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 11 You are reading this latest preprint version Abstract Glycolysis is essential for cellular energy production, making its enzymes attractive antimicrobial targets. Traditional strategies targeting conserved catalytic sites risk host toxicity due to limited species specificity. Allosteric sites—spatially distinct, evolutionarily divergent regulatory regions—offer selective inhibition but are challenging to detect experimentally. Here, we systematically mapped allosteric sites across all ten glycolytic enzymes of Staphylococcus aureus and Plasmodium vivax using a multi-scale computational framework combining elastic network models, residue interaction networks, and complementary machine-learning algorithms. High-confidence allosteric sites were identified in fructose-1,6-bisphosphate aldolase, triosephosphate isomerase, and phosphoglycerate mutase, revealing diverse regulatory architectures, from interfacial network hubs to hinge-mediated dynamic control. Experimentally validated sites in pyruvate kinase and phosphofructokinase further reinforced the predictive framework. Comparative analysis with human homologs confirmed pronounced species-specific divergence, supporting selective targeting. Virtual screening 1,615 FDA-approved compounds across all ten enzymes identified multi-target ligands exhibiting amphiphilic, interface-stabilizing architectures capable of coordinated glycolytic modulation. Binding analyses revealed a balanced contribution of polar and hydrophobic interactions, consistent with robust allosteric modulation. This pathway-wide, network-informed approach demonstrates the feasibility of selectively disrupting bacterial glycolysis and provides a blueprint for rational polypharmacology and next-generation antimicrobial design. Glycolysis Allosteric regulation Staphylococcus aureus Drug repurposing species-specificity polypharmacology virtual screening elastic network model Full Text Additional Declarations No competing interests reported. Supplementary Files Supplementary.docx Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 08 Apr, 2026 Reviews received at journal 07 Apr, 2026 Reviews received at journal 05 Apr, 2026 Reviewers agreed at journal 05 Apr, 2026 Reviews received at journal 04 Apr, 2026 Reviewers agreed at journal 31 Mar, 2026 Reviewers agreed at journal 30 Mar, 2026 Reviewers invited by journal 30 Mar, 2026 Editor assigned by journal 30 Mar, 2026 Submission checks completed at journal 18 Mar, 2026 First submitted to journal 17 Mar, 2026 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. 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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-9149499","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":614987363,"identity":"d0bd3a08-29a1-48ab-9f77-1943bd907446","order_by":0,"name":"Latife Sude Vural","email":"","orcid":"","institution":"Kadir Has University","correspondingAuthor":false,"prefix":"","firstName":"Latife","middleName":"Sude","lastName":"Vural","suffix":""},{"id":614987364,"identity":"002c2066-fba6-4a4e-8e4b-581f93c9a259","order_by":1,"name":"Elcin Kahraman","email":"","orcid":"","institution":"Kadir Has 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Traditional strategies targeting conserved catalytic sites risk host toxicity due to limited species specificity. Allosteric sites\u0026mdash;spatially distinct, evolutionarily divergent regulatory regions\u0026mdash;offer selective inhibition but are challenging to detect experimentally. Here, we systematically mapped allosteric sites across all ten glycolytic enzymes of \u003cem\u003eStaphylococcus aureus\u003c/em\u003e and \u003cem\u003ePlasmodium vivax\u003c/em\u003e using a multi-scale computational framework combining elastic network models, residue interaction networks, and complementary machine-learning algorithms. High-confidence allosteric sites were identified in fructose-1,6-bisphosphate aldolase, triosephosphate isomerase, and phosphoglycerate mutase, revealing diverse regulatory architectures, from interfacial network hubs to hinge-mediated dynamic control. 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