Principal Component Analysis Based Clustering of Insecticides and Molecular Docking of Pyrethroids Insecticides

Principal Component Analysis Based Clustering of Insecticides and Molecular Docking of Pyrethroids Insecticides | 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 Principal Component Analysis Based Clustering of Insecticides and Molecular Docking of Pyrethroids Insecticides Kahksha Ahmed, Afshan Ahmed, Jalaluddin Khan, Puneet Garg, Soumita Seth, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7312651/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 Background: Insecticides are the chemical substances used to control pest in agriculture and domestic purpose, structural variations among insecticides leads to the change in the safety profile and application, in silico molecular docking studies are used to explain the mechanism of action of chemical substance on the specific target. Principal component analysis is a statistical method used to extract unique features from the large dataset. Methods : We made an investigation to find out correlation on the safety profile of insecticides in terms of acute toxicity, irritant, health hazard, and environmental hazard using principal component analysis (PCA), a dataset was prepared from available literature for 55 insecticides, their safety profile were retrieved from PubChem, PCA was performed on the prepared dataset using excel state software. ADME analysis was performed on the pyrethroids group of compounds using an online server-based docking as well as we had also performed molecular docking on the pyrethroids group of compounds cypermethrin, allethrin, resmethrin, and permethrin insecticides, with voltage-gated sodium ion channel and caspase-3 protein was retrieved from protein data bank PDB ID 2A79, and 1RE1, molecular docking was carried out using Auto Dock vina 4.2, discovery studio and open babel software. Results: Library of 55 insecticidal compounds was prepared their safety profile was obtained and PCA was performed on the dataset which shows that irritant and environmentFal hazard properties of insecticides largely affect the dataset. Server-based ADME analysis showed that cypermethrin is the least toxic compound among different pyrethroids. On the basis of In silico molecular docking permethrin was found to have maximum binding affinity -7.3 kcal/mol followed by cypermethrin, resmethrin, -7.2 kcal/mol, and the least binding affinity was observed with allethrin for 2a79 receptor -5.5 kcal/mol. Molecular docking on caspase-3 enzyme shows that maximum enzyme inhibition was achieved with cypermethrin and resmethrin -7.6 kcal/mol followed by permethrin -6.4 and least with allethrin 6.1 kcal/mol. Conclusion: Multivariate PCA showed that the environmental hazard and irritant properties are predominantly present among different classes of insecticides, ADME analysis showed that cypermethrin is the least toxic compound to human as compared to other pyrethroids, and in silico studies showed maximum activity with permethrin for 2a79 receptor and cypermethrin and resmethrin for 1RE1 receptor. Principal component analysis Insecticide In silico molecular docking Voltage-Gated Sodium-Ion channel chilibot 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-7312651","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":502509354,"identity":"9a1fa7b5-b387-400e-90c0-975db37628df","order_by":0,"name":"Kahksha Ahmed","email":"","orcid":"","institution":"St. Andrews Institute of Technology \u0026 Management","correspondingAuthor":false,"prefix":"","firstName":"Kahksha","middleName":"","lastName":"Ahmed","suffix":""},{"id":502509356,"identity":"a4112fe6-8c6d-4830-8353-46ba17e042c8","order_by":1,"name":"Afshan Ahmed","email":"","orcid":"","institution":"School of Pharmaceutical Education 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Arizona","correspondingAuthor":false,"prefix":"","firstName":"Saurav","middleName":"","lastName":"Mallik","suffix":""}],"badges":[],"createdAt":"2025-08-06 19:38:07","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7312651/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7312651/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":91060857,"identity":"ada82eaf-be4e-4ec6-9382-63acb0089cc7","added_by":"auto","created_at":"2025-09-11 08:54:15","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1088224,"visible":true,"origin":"","legend":"","description":"","filename":"afshanPCAdockingPuneetsmRevisedv2.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7312651/v1_covered_a8b0b467-2c56-4d3d-9e74-592776f25c53.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Principal Component Analysis Based Clustering of Insecticides and Molecular Docking of Pyrethroids Insecticides","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"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":"Principal component analysis, Insecticide, In silico molecular docking, Voltage-Gated Sodium-Ion channel, chilibot","lastPublishedDoi":"10.21203/rs.3.rs-7312651/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7312651/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground:\u003c/strong\u003e Insecticides are the chemical substances used to control pest in agriculture and domestic purpose, structural variations among insecticides leads to the change in the safety profile and application, \u003cem\u003ein silico \u003c/em\u003emolecular docking studies are used to explain the mechanism of action of chemical substance on the specific target. Principal component analysis is a \u003cstrong\u003estatistical\u003c/strong\u003e method used to extract unique features from the large dataset.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eMethods\u003c/strong\u003e: We made an investigation to find out correlation on the safety profile of insecticides in terms of acute toxicity, irritant, health hazard, and environmental hazard using principal component analysis (PCA), a dataset was prepared from available literature for 55 insecticides, their safety profile were retrieved from PubChem, PCA was performed on the prepared dataset using excel state software. ADME analysis was performed on the pyrethroids group of compounds using an online server-based docking as well as we had also performed molecular docking on the pyrethroids group of compounds cypermethrin, allethrin, resmethrin, and permethrin insecticides, with voltage-gated sodium ion channel and caspase-3 protein was retrieved from protein data bank PDB ID 2A79, and 1RE1, molecular docking was carried out using Auto Dock vina 4.2, discovery studio and open babel software.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eResults: \u003c/strong\u003eLibrary of 55 insecticidal compounds was prepared their safety profile was obtained and PCA was performed on the dataset which shows that irritant and environmentFal hazard properties of insecticides largely affect the dataset. Server-based ADME analysis showed that cypermethrin is the least toxic compound among different pyrethroids. On the basis of \u003cem\u003eIn silico\u003c/em\u003e molecular docking \u003cstrong\u003epermethrin was found to have maximum binding affinity -7.3 kcal/mol\u003c/strong\u003e followed by cypermethrin, resmethrin, -7.2 kcal/mol, and the least binding affinity was observed with allethrin for 2a79 receptor -5.5 kcal/mol. Molecular docking on caspase-3 enzyme shows that maximum enzyme inhibition was achieved with cypermethrin and resmethrin -7.6 kcal/mol followed by \u003cstrong\u003epermethrin -6.4\u003c/strong\u003eand least with allethrin 6.1 kcal/mol.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusion: \u003c/strong\u003eMultivariate PCA showed that the environmental hazard and irritant properties are predominantly present among different classes of insecticides, ADME analysis showed that cypermethrin is the least toxic compound to human as compared to other pyrethroids, and \u003cem\u003ein silico\u003c/em\u003e studies showed maximum activity with permethrin for 2a79 receptor and cypermethrin and resmethrin for 1RE1 receptor.\u003c/p\u003e","manuscriptTitle":"Principal Component Analysis Based Clustering of Insecticides and Molecular Docking of Pyrethroids Insecticides","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-09-11 08:46:08","doi":"10.21203/rs.3.rs-7312651/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":"9755d2de-745b-48a3-a65d-5dbfad5f5fe7","owner":[],"postedDate":"September 11th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-09-11T08:46:08+00:00","versionOfRecord":[],"versionCreatedAt":"2025-09-11 08:46:08","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7312651","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7312651","identity":"rs-7312651","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}