In Silico Discovery of Thioglycoside Analogues as Donor-Site Inhibitors of Glycosyltransferase LgtC

In Silico Discovery of Thioglycoside Analogues as Donor-Site Inhibitors of Glycosyltransferase LgtC | 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 In Silico Discovery of Thioglycoside Analogues as Donor-Site Inhibitors of Glycosyltransferase LgtC Olimpo Sierra-Hernandez, Oscar Saurith-Coronell, Jackson J. Alcázar, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8233121/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 17 Mar, 2026 Read the published version in Scientific Reports → Version 1 posted 12 You are reading this latest preprint version Abstract The growing prevalence of multidrug-resistant Gram-negative pathogens highlights the urgent need for therapeutic strategies that complement traditional antibiotics by targeting essential virulence pathways. Glycosyltransferase LgtC, a key enzyme in lipooligosaccharide (LOS) biosynthesis, represents an attractive target for antivirulence approaches because of its essential role in bacterial immune evasion and pathogenicity. In this work, we employed an integrated in silico pipeline to identify thioglycoside analogs structurally related to the metabolic decoys FucSBn and BacSBn, evaluating their potential to hit the UDP-galactose donor pocket of LgtC. A similarity-based screening in PubChem, followed by ADME–Tox filtering yield 18 candidate analogs. Molecular docking using AutoDock-GPU revealed several candidates, most notably C-5 (− 8.36 kcal/mol) and C-18 (− 8.13 kcal/mol), to bind favorably within the donor site, showing more negative mean scoring values than natural donor UDP-α-D-galactose (− 6.74 kcal/mol). Redocking of the natural ligand reproduced the crystallographic pose, supporting the reliability of the docking protocol. To assess dynamic behavior, 100 ns molecular dynamics simulations (AMBER14) were performed for each complex. The top-scoring analogs maintained stable binding poses, with RMSD values of ~ 2.0–3.0 Å and preserved donor-like hydrogen-bond networks complemented by π-stacking and sulfur-mediated contacts. These interaction patterns suggest that the thioglycoside analogs may occupy the donor site in a manner compatible with competitive binding. While docking and MD describe different aspects of ligand recognition, several trends observed in docking, such as the favorable binding scores of C-5 and C-18, are broadly consistent with their ability to maintain stable poses during MD. Based on this consistency and scoring, the thioglycoside scaffolds C-5, C-14, and C-18 emerge as computationally prioritized candidates for subsequent biochemical testing against LgtC. Furthermore, these scaffolds offer a mechanistic basis and putative starting points for future structure-based optimization of thioglycoside analogs aimed at disrupting LOS biosynthesis in multidrug-resistant Gram-negative bacteria. Biological sciences/Biochemistry Biological sciences/Computational biology and bioinformatics Biological sciences/Drug discovery Biological sciences/Structural biology Thioglycoside analogues Glycosyltransferase LgtC inhibition In silico drug discovery Antivirulence strategy Gram-negative bacteria Full Text Additional Declarations No competing interests reported. Supplementary Files SupportingMaterial.zip Cite Share Download PDF Status: Published Journal Publication published 17 Mar, 2026 Read the published version in Scientific Reports → Version 1 posted Editorial decision: Revision requested 09 Jan, 2026 Reviews received at journal 25 Dec, 2025 Reviewers agreed at journal 16 Dec, 2025 Reviews received at journal 15 Dec, 2025 Reviewers agreed at journal 15 Dec, 2025 Reviewers agreed at journal 15 Dec, 2025 Reviewers agreed at journal 15 Dec, 2025 Reviewers invited by journal 11 Dec, 2025 Editor assigned by journal 11 Dec, 2025 Editor invited by journal 09 Dec, 2025 Submission checks completed at journal 07 Dec, 2025 First submitted to journal 07 Dec, 2025 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-8233121","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":561164289,"identity":"7f7dcd78-adfc-4c4d-a306-c60410a102e0","order_by":0,"name":"Olimpo Sierra-Hernandez","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA4UlEQVRIiWNgGAWjYDACdsYGECXHwABhgIABfi3MEJXGUC0GxGiBUIkNSBbg18LPzNy6uaCiLn3D7ea2Bx/3/JFjYG/eJsFQY4NTi2QzY9vtGWcO5264c7DdcMYzA2MGnmNlEgzH0nBqMTgM1MLbdiB3w43ENmmeAwaJDRI5ZhKMDYcJaalLN4BqqW+Qf0OUFuYEmJYEBgke/FpgfjGcCdQiOeOAsWEbT1qxRQIev/Cztz+7DQwxeb4b6c8kPhyQk+dnP7zxxgc8IQYCzCg8NhCRgFcDupZRMApGwSgYBegAAJ1EUUhvXLxwAAAAAElFTkSuQmCC","orcid":"","institution":"Universidad del Norte","correspondingAuthor":true,"prefix":"","firstName":"Olimpo","middleName":"","lastName":"Sierra-Hernandez","suffix":""},{"id":561164290,"identity":"68e9562e-9748-446e-9e19-5ad6c00c7b4f","order_by":1,"name":"Oscar Saurith-Coronell","email":"","orcid":"","institution":"Universidad del Norte","correspondingAuthor":false,"prefix":"","firstName":"Oscar","middleName":"","lastName":"Saurith-Coronell","suffix":""},{"id":561164291,"identity":"21142204-0ab8-42df-9fca-761dec21f013","order_by":2,"name":"Jackson J. 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LgtC","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific Reports","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Thioglycoside analogues, Glycosyltransferase LgtC inhibition, In silico drug discovery, Antivirulence strategy, Gram-negative bacteria","lastPublishedDoi":"10.21203/rs.3.rs-8233121/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8233121/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThe growing prevalence of multidrug-resistant Gram-negative pathogens highlights the urgent need for therapeutic strategies that complement traditional antibiotics by targeting essential virulence pathways. Glycosyltransferase LgtC, a key enzyme in lipooligosaccharide (LOS) biosynthesis, represents an attractive target for antivirulence approaches because of its essential role in bacterial immune evasion and pathogenicity. In this work, we employed an integrated \u003cem\u003ein silico\u003c/em\u003e pipeline to identify thioglycoside analogs structurally related to the metabolic decoys FucSBn and BacSBn, evaluating their potential to hit the UDP-galactose donor pocket of LgtC. A similarity-based screening in PubChem, followed by ADME\u0026ndash;Tox filtering yield 18 candidate analogs. Molecular docking using AutoDock-GPU revealed several candidates, most notably C-5 (\u0026minus;\u0026thinsp;8.36 kcal/mol) and C-18 (\u0026minus;\u0026thinsp;8.13 kcal/mol), to bind favorably within the donor site, showing more negative mean scoring values than natural donor UDP-α-D-galactose (\u0026minus;\u0026thinsp;6.74 kcal/mol). Redocking of the natural ligand reproduced the crystallographic pose, supporting the reliability of the docking protocol. To assess dynamic behavior, 100 ns molecular dynamics simulations (AMBER14) were performed for each complex. The top-scoring analogs maintained stable binding poses, with RMSD values of ~\u0026thinsp;2.0\u0026ndash;3.0 \u0026Aring; and preserved donor-like hydrogen-bond networks complemented by π-stacking and sulfur-mediated contacts. These interaction patterns suggest that the thioglycoside analogs may occupy the donor site in a manner compatible with competitive binding. While docking and MD describe different aspects of ligand recognition, several trends observed in docking, such as the favorable binding scores of C-5 and C-18, are broadly consistent with their ability to maintain stable poses during MD. Based on this consistency and scoring, the thioglycoside scaffolds C-5, C-14, and C-18 emerge as computationally prioritized candidates for subsequent biochemical testing against LgtC. Furthermore, these scaffolds offer a mechanistic basis and putative starting points for future structure-based optimization of thioglycoside analogs aimed at disrupting LOS biosynthesis in multidrug-resistant Gram-negative bacteria.\u003c/p\u003e","manuscriptTitle":"In Silico Discovery of Thioglycoside Analogues as Donor-Site Inhibitors of Glycosyltransferase LgtC","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-12-17 12:19:41","doi":"10.21203/rs.3.rs-8233121/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2026-01-09T11:10:03+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-12-26T01:21:15+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"40698558508966355431983965388109115024","date":"2025-12-16T12:09:02+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-12-16T03:44:56+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"33139983081818449450573575250622921581","date":"2025-12-15T14:00:35+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"161916192441168825782516601395661105769","date":"2025-12-15T11:44:18+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"243602728000550000661523609969343892480","date":"2025-12-15T07:43:26+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-12-12T00:58:50+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-12-11T15:07:32+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-12-09T10:02:24+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-12-07T05:10:40+00:00","index":"","fulltext":""},{"type":"submitted","content":"Scientific Reports","date":"2025-12-07T05:02:59+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific Reports","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"82e669ee-f93e-40cd-bd6d-cd457210e004","owner":[],"postedDate":"December 17th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":59746407,"name":"Biological sciences/Biochemistry"},{"id":59746408,"name":"Biological sciences/Computational biology and bioinformatics"},{"id":59746409,"name":"Biological sciences/Drug discovery"},{"id":59746410,"name":"Biological sciences/Structural biology"}],"tags":[],"updatedAt":"2026-03-23T16:01:25+00:00","versionOfRecord":{"articleIdentity":"rs-8233121","link":"https://doi.org/10.1038/s41598-026-43638-x","journal":{"identity":"scientific-reports","isVorOnly":false,"title":"Scientific Reports"},"publishedOn":"2026-03-17 15:58:41","publishedOnDateReadable":"March 17th, 2026"},"versionCreatedAt":"2025-12-17 12:19:41","video":"","vorDoi":"10.1038/s41598-026-43638-x","vorDoiUrl":"https://doi.org/10.1038/s41598-026-43638-x","workflowStages":[]},"version":"v1","identity":"rs-8233121","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8233121","identity":"rs-8233121","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}