Design and Synthesis of Benzylidene Phenylacetamide-based Derivatives as Potential Antibacterial Agents Targeting Staphylococcus Aureus Thymidylate Kinase

Design and Synthesis of Benzylidene Phenylacetamide-based Derivatives as Potential Antibacterial Agents Targeting Staphylococcus Aureus Thymidylate Kinase | 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 Design and Synthesis of Benzylidene Phenylacetamide-based Derivatives as Potential Antibacterial Agents Targeting Staphylococcus Aureus Thymidylate Kinase ABDUL BAQI, KOPPULA JAYANTHI, M MUTHUKUMARAN This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9016290/v1 This work is licensed under a CC BY 4.0 License Status: Under Revision Version 1 posted 16 You are reading this latest preprint version Abstract Objective : There has been a significant global surge in antimicrobial resistance in recent years, with Staphylococcus aureus infections proving particularly challenging to treat. The bacterium has resisted various antibiotics, including β-lactams. The primary objective is to identify antibacterial agents targeting Staphylococcus aureus Thymidylate kinase (TMK). Methods: Six molecules were conceived through a process involving molecular docking (glide module), Qikprop screening for ADME (absorption, distribution, metabolism, and excretion) prediction, and prime MMGBSA (Molecular Mechanics Generalized Born Surface Area) analysis to assess binding free energy employing Schrödinger suite 2021-4. in -vitro studies MIC, MBC, and TIME KILL were performed to evaluate the antibacterial activity. The designed molecules are evaluated based on glide score binding affinity and in-vitro results. Findings: The six molecules exhibited hydrophobic and hydrogen bonding interactions with the Staphylococcus aureus Thymidylate kinase (4HLC.pdb). Thymidylate kinase (TMK) enzyme, as identified in the Protein Data Bank entry. Among these, compound C 3 displayed XP-docking Glide score and ΔBind of -4.39 kcal/mol and -76.93 kcal/mol respectively. To explore the dynamic behaviour of the C 3 /4HLC complex, a 100-nanosecond molecular dynamics simulation was conducted. Gram-positive strains of S. aureus (NCIM 5021) Ic 50 values (1.91 µM), clinical MRSA strains (ATCC 43300) Ic 50 values (3.91 µM) shown in the in-vitro study. Interpretation: Based on all studies in the performance of C 3 demonstrated with favourable outcomes, Benzylidene phenyl acetamide-based derivatives are anticipated to be potential future inhibitors of the SATMK , suggesting their potential role as antibacterial agents. Funding: We have no funding for this project. Full Text Additional Declarations Competing interest reported. no Cite Share Download PDF Status: Under Revision Version 1 posted Editorial decision: Revision requested 19 Mar, 2026 Reviews received at journal 16 Mar, 2026 Reviews received at journal 14 Mar, 2026 Reviews received at journal 13 Mar, 2026 Reviews received at journal 13 Mar, 2026 Reviewers agreed at journal 09 Mar, 2026 Reviewers agreed at journal 09 Mar, 2026 Reviewers agreed at journal 09 Mar, 2026 Reviewers agreed at journal 05 Mar, 2026 Reviewers agreed at journal 05 Mar, 2026 Reviewers agreed at journal 04 Mar, 2026 Reviewers agreed at journal 04 Mar, 2026 Reviewers invited by journal 04 Mar, 2026 Editor assigned by journal 03 Mar, 2026 Submission checks completed at journal 03 Mar, 2026 First submitted to journal 03 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. 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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-9016290","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":602175727,"identity":"5f5eb74e-3858-4fd9-a8af-6dd46b013a6e","order_by":0,"name":"ABDUL BAQI","email":"","orcid":"","institution":"Sri Blaji Vidyapeeth School of Pharmacy","correspondingAuthor":false,"prefix":"","firstName":"ABDUL","middleName":"","lastName":"BAQI","suffix":""},{"id":602175728,"identity":"3c9ded08-fe62-49fb-8457-b0a135571d24","order_by":1,"name":"KOPPULA JAYANTHI","email":"data:image/png;base64,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","orcid":"","institution":"Sri Blaji Vidyapeeth School of Pharmacy","correspondingAuthor":true,"prefix":"","firstName":"KOPPULA","middleName":"","lastName":"JAYANTHI","suffix":""},{"id":602175730,"identity":"e340a076-0f72-4495-bdea-51e5ee8e236c","order_by":2,"name":"M MUTHUKUMARAN","email":"","orcid":"","institution":"Sri Blaji Vidyapeeth School of Pharmacy","correspondingAuthor":false,"prefix":"","firstName":"M","middleName":"","lastName":"MUTHUKUMARAN","suffix":""}],"badges":[],"createdAt":"2026-03-03 05:53:31","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-9016290/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-9016290/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":104779497,"identity":"59c5837e-b478-43a7-9ed0-35436d14d294","added_by":"auto","created_at":"2026-03-17 07:41:03","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1299001,"visible":true,"origin":"","legend":"","description":"","filename":"synthesispapernew1.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9016290/v1_covered_fbe9cb95-a019-4dd6-9718-1c4cc13cee02.pdf"}],"financialInterests":"Competing interest reported. no","formattedTitle":"\u003cp\u003eDesign and Synthesis of Benzylidene Phenylacetamide-based Derivatives as Potential Antibacterial Agents Targeting Staphylococcus Aureus Thymidylate Kinase\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"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":"in-silico-pharmacology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"insp","sideBox":"Learn more about [In Silico Pharmacology](https://link.springer.com/journal/40203)","snPcode":"40203","submissionUrl":"https://submission.nature.com/new-submission/40203/3","title":"In Silico Pharmacology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-9016290/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-9016290/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eObjective \u003c/strong\u003e: There has been a significant global surge in antimicrobial resistance in recent years, with Staphylococcus aureus infections proving particularly challenging to treat. The bacterium has resisted various antibiotics, including β-lactams. The primary objective is to identify antibacterial agents targeting \u003cem\u003eStaphylococcus aureus\u003c/em\u003e Thymidylate kinase (TMK).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eMethods: \u003c/strong\u003eSix molecules were conceived through a process involving molecular docking (glide module), Qikprop screening for ADME (absorption, distribution, metabolism, and excretion) prediction, and prime MMGBSA (Molecular Mechanics Generalized Born Surface Area) analysis to assess binding free energy employing Schrödinger suite 2021-4. \u0026nbsp;in\u003cem\u003e-vitro\u003c/em\u003e studies MIC, MBC, and TIME KILL were performed to evaluate the antibacterial activity. The designed molecules are evaluated based on glide score binding affinity and \u003cem\u003ein-vitro\u003c/em\u003e results.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFindings: \u003c/strong\u003eThe six molecules exhibited hydrophobic and hydrogen bonding interactions with the \u003cem\u003eStaphylococcus aureus\u003c/em\u003e Thymidylate kinase (4HLC.pdb). Thymidylate kinase (TMK) enzyme, as identified in the Protein Data Bank entry. Among these, compound C\u003csub\u003e3\u003c/sub\u003e displayed XP-docking Glide score and ΔBind of -4.39 kcal/mol and -76.93 kcal/mol respectively. To explore the dynamic behaviour of the C\u003csub\u003e3\u003c/sub\u003e/4HLC complex, a 100-nanosecond molecular dynamics simulation was conducted. Gram-positive strains of \u003cem\u003eS. aureus\u003c/em\u003e (NCIM 5021) Ic\u003csub\u003e50 \u003c/sub\u003evalues (1.91 µM), clinical \u003cem\u003eMRSA\u003c/em\u003e strains (ATCC 43300) Ic\u003csub\u003e50 \u003c/sub\u003evalues (3.91 µM) shown in the in-vitro study.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eInterpretation: \u003c/strong\u003eBased on all studies in\u003cstrong\u003e \u003c/strong\u003ethe performance of C\u003csub\u003e3\u003c/sub\u003e demonstrated with favourable outcomes, Benzylidene phenyl acetamide-based derivatives are anticipated to be potential future inhibitors of the \u003cem\u003eSATMK\u003c/em\u003e, suggesting their potential role as antibacterial agents.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding:\u0026nbsp; \u003c/strong\u003eWe have no funding for this project.\u0026nbsp;\u003c/p\u003e","manuscriptTitle":"Design and Synthesis of Benzylidene Phenylacetamide-based Derivatives as Potential Antibacterial Agents Targeting Staphylococcus Aureus Thymidylate Kinase","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-03-09 15:44:26","doi":"10.21203/rs.3.rs-9016290/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2026-03-19T06:10:02+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-03-16T12:23:09+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-03-14T04:45:30+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-03-13T17:11:26+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-03-13T05:01:07+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"192201363985170561801811362380663392762","date":"2026-03-10T02:35:45+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"89636837029579331440272660920977021184","date":"2026-03-09T13:29:09+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"171753003322599715497795422600999986623","date":"2026-03-09T07:35:01+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"220331899479935983287366073454680662098","date":"2026-03-05T23:12:39+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"285725897007987105032346508162184540520","date":"2026-03-05T14:33:19+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"4291282210459639425357472066843362353","date":"2026-03-05T04:16:09+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"19823207672354386218601892346564643685","date":"2026-03-05T03:32:44+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2026-03-05T02:33:39+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-03-03T09:52:21+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-03-03T09:47:50+00:00","index":"","fulltext":""},{"type":"submitted","content":"In Silico Pharmacology","date":"2026-03-03T05:40:12+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"in-silico-pharmacology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"insp","sideBox":"Learn more about [In Silico Pharmacology](https://link.springer.com/journal/40203)","snPcode":"40203","submissionUrl":"https://submission.nature.com/new-submission/40203/3","title":"In Silico Pharmacology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"08469a9b-962e-47b1-bd5f-fb1d16c59231","owner":[],"postedDate":"March 9th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"in-revision","subjectAreas":[],"tags":[],"updatedAt":"2026-03-19T06:25:32+00:00","versionOfRecord":[],"versionCreatedAt":"2026-03-09 15:44:26","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-9016290","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-9016290","identity":"rs-9016290","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}