Molecular docking analysis of LuxR with Octylbenzene

Molecular docking analysis of LuxR with Octylbenzene | 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Article Molecular docking analysis of LuxR with Octylbenzene Pankaj Kumar, Srishti Singh This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7942069/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 LuxR-type transcriptional regulators mediate quorum sensing (QS) in Gram-negative bacteria by binding acyl-homoserine lactones (AHLs). Therefore, it is of interest to describe the molecular docking analysis of LuxR with octylbenzene (CID:16607), a non-natural hydrophobic ligand. AutoDock Vina predicted a stable pose (–3.0 kcal/mol) involving Tyr62, Trp66, and Glu64, while native AHL docking showed stronger affinity (–7.1 kcal/mol). Despite its moderate affinity, octylbenzene occupied a similar binding pocket, highlighting hydrophobic scaffolds as potential quorum-sensing inhibitors. Bioinformatics LuxR quorum sensing docking AutoDock Vina hydrophobic ligand octylbenzene PyMOL AHL mimic Figures Figure 1 1. Background Quorum sensing (QS) is a cell-density dependent communication mechanism in bacteria that enables coordinated expression of genes involved in functions like virulence, biofilm formation, and motility [ 1 ]. In Gram-negative bacteria, this communication relies on small diffusible molecules called acyl-homoserine lactones (AHLs) [ 2 ]. LuxR-type transcriptional regulators are key components of this system, binding AHLs to initiate QS gene activation [ 3 ]. Targeting LuxR with synthetic or non-canonical ligands provides a strategy to interfere with bacterial communication, offering alternatives to antibiotics [ 4 ]. Octylbenzene is a hydrophobic aromatic molecule with potential to mimic the nonpolar tail of long-chain AHLs [ 5 ]. Hydrophobic AHL mimics are of interest because they may exhibit greater environmental stability and resist enzymatic degradation, making them promising leads for anti-virulence therapies against quorum-sensing-dependent pathogens [ 6 ]. Therefore, it is of interest to report the Molecular docking analysis of LuxR with Octylbenzene. 2. Materials and Methods 2.1. Ligand Selection and Properties Octylbenzene (CID: 16607) was selected from PubChem due to its hydrophobic, linear tail-like structure resembling long-chain AHLs. Its molecular weight is 198.3 g/mol, chemical formula C₁₄H₂₂, and logP is approximately 5.7. The SMILES notation is "CCCCCCCC1=CC=CC=C1". Its physicochemical profile suggests compatibility with nonpolar protein pockets [5] . 2.2. Receptor Preparation The LuxR receptor model was derived from a homology-based structure using PDB template 3QP5 [ 7 ]. The PDB structure was cleaned in PyMOL [8] by removing water and non-standard residues. AutoDock Tools (v1.5.7) was used to prepare the receptor by adding polar hydrogens and computing Gasteiger charges. The final file was saved in .pdbqt format as luxr_clean.pdbqt. 2.3. Ligand Preparation Octylbenzene was downloaded in .sdf format from PubChem and converted to .pdbqt using Open Babel (v3.1.1). It was energy-minimized and hydrogens were added using AutoDock Tools [5,8] . 2.4. Docking Protocol Docking was performed using AutoDock Vina (v1.1.2) [9] with the following parameters: Grid center: X = –3.793, Y = –3.755, Z = 15.901 Grid size: 20 × 20 × 20 Å Exhaustiveness: default CPUs used: 8 Ligand: ahl.pdbqt Receptor: luxr_clean.pdbqt Output: docked_luxr_ahl.pdbqt The docking log (vina_log.txt) showed successful convergence. The top-ranked pose had a binding affinity of –3.0 kcal/mol with 0.0 Å RMSD, indicating a stable and unique interaction. 2.5. Visualization and Interaction Analysis The docking pose was visualized using PyMOL (v2.5). Residues within 5 Å were identified and labeled. 2D interaction diagrams were generated using Discovery Studio Visualizer 2021. Residue-level interaction annotations were based on chemical properties and spatial proximity. 3. Results and Discussion Molecular docking revealed a well-defined pose of octylbenzene (orange sticks) embedded within the hydrophobic pocket of LuxR (cyan cartoon) (Figure 1). The aromatic ring of Tyr40 aligns favorably with the ligand’s aromatic ring, suggesting π–π stacking. Glu64, Lys65, and Ser116 appear to stabilize the ligand edges through polar or electrostatic interactions, while Trp66, Tyr62, and Pro63 form a hydrophobic shell around the ligand. The presence of multiple aromatic residues supports strong π–π and van der Waals interactions. Glu115 and Ser116 contribute to conformational stabilization. Despite weaker binding (–3.0 kcal/mol vs –7.1 kcal/mol for AHL), octylbenzene docked in the same pocket, indicating potential competitive inhibition. The findings indicate that hydrophobic molecules like octylbenzene can engage LuxR’s binding site in a manner comparable to native AHLs, supporting their use as scaffolds for quorum-sensing inhibitor design. Table 1. Predicted Residue–Ligand Interactions in the LuxR–Octylbenzene Complex Residue Type Properties Likely Interaction TYR40 Aromatic Polar OH group + aromatic ring π–π stacking, H-bond potential ASN61 Polar Side-chain amide Possible H-bond acceptor TYR62 Aromatic Aromatic + polar OH π–π stacking / H-bond PRO63 Nonpolar Aliphatic, rigid structure Van der Waals GLU64 Charged Acidic (COO–) Electrostatic (with polar atoms) LYS65 Charged Basic (NH₃⁺) May stabilize ligand edge TRP66 Aromatic Hydrophobic + π-system Strong π–π or van der Waals GLU115 Charged Acidic Distant stabilizer or steric limiter SER116 Polar OH side chain Hydrogen bond donor GLY117 Neutral Flexible backbone Structural support Residues were identified using spatial selection within 5 Å and analyzed using PyMOL. 4. Conclusion The interaction of LuxR with octylbenzene, a non-canonical, hydrophobic ligand is described. Docking analysis revealed stable binding involving key residues such as Tyr62, Trp66, Glu64, and Ser116. The pose resembled known AHL–LuxR interactions, indicating that hydrophobic AHL mimics could act as quorum-sensing inhibitors. Although the predicted binding affinity is moderate, such ligands may still competitively occupy the binding site, warranting further validation through molecular dynamics simulations and in vitro assays. Limitations This study is limited to in silico docking analysis. While docking scores provide an initial estimate of binding potential, further validation through molecular dynamics simulations and biochemical assays is required to confirm functional inhibition of LuxR. Declarations Ethical Compliance This work adheres to the ethical guidelines of ICAR–IARI, New Delhi. Institutional approval was obtained for the study. Acknowledgements The authors would like to thank the Indian Agricultural Research Institute (ICAR–IARI), New Delhi, for providing access to computational facilities and support during this study. We are grateful to Dr. Anupama Singh, Joint Director (Education), ICAR–IARI, for guidance on ethical compliance. The authors acknowledges support from the institutional library resources for literature access. The authors also thank their colleagues for valuable discussions and technical assistance in molecular docking and visualization. Data Availability All data, scripts, and figure files used in this study are publicly available at the following GitHub repository: https://github.com/pankaj357/LuxR_Docking_Project References Whitehead NA et al. FEMS Microbiol Rev. 2001 25:365 [PMID:11524130]. Vannini A et al. EMBO J. 2002 21:4393 [PMID:12198141]. Galloway WRJD et al. Chem Rev. 2011 111:28 [PMID:21182299]. Hentzer M et al. EMBO J. 2003 22:3803 [PMID:12881415]. PubChem. Compound Summary for CID 16607, Octylbenzene. https://pubchem.ncbi.nlm.nih.gov/compound/16607 Kalia VC. Biotechnol Adv. 2013 31:224 [PMID:23142623]. Berman HM et al. Nucleic Acids Res. 2000 28:235 [PMID:10592235]. Schrödinger LLC. PyMOL Molecular Graphics System, v2.5. 2021. https://pymol.org Trott O & Olson AJ. J Comput Chem. 2010 31:455 [PMID:19499576]. Additional Declarations The authors declare no competing interests. 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-7942069","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":534585148,"identity":"5e00369e-6332-49bb-b3d7-a311cf7e67a0","order_by":0,"name":"Pankaj Kumar","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAxUlEQVRIiWNgGAWjYBAC9gYwlSAHIg88IEYLzzGIFmOwlgRStCSCbSNOi3wD24OfO9LS54cdfgi0xU5Ot4GQFjYGdsPeMzm5G2+nGQC1JBubHSCgxZ6NgU2Ct60id+PsBJCWA4nbCGkB2sIm+betIt1wdvoH4rVI87blJMhL5xBtS2K7sWxbmuEG6ZyCAwkGRPiFh/nwsYdv25Ll5Wenb/7wocJOjqAWBgbGNjBlAFZpQFA5GLCBSfkG4lSPglEwCkbBCAQAv/dA1VrRqtcAAAAASUVORK5CYII=","orcid":"https://orcid.org/0009-0006-3422-8881","institution":"Indian Agriculture Research Institute, New Delhi","correspondingAuthor":true,"prefix":"","firstName":"Pankaj","middleName":"","lastName":"Kumar","suffix":""},{"id":534585154,"identity":"eee0bf56-fabd-4d5e-aa26-cf3503e1c46f","order_by":1,"name":"Srishti Singh","email":"","orcid":"","institution":"Indian Agriculture Research Institute, New Delhi","correspondingAuthor":false,"prefix":"","firstName":"Srishti","middleName":"","lastName":"Singh","suffix":""}],"badges":[],"createdAt":"2025-10-25 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18:16:11","extension":"html","order_by":6,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":29005,"visible":true,"origin":"","legend":"","description":"","filename":"earlyproof.html","url":"https://assets-eu.researchsquare.com/files/rs-7942069/v1/71047399de166b3e55310689.html"},{"id":94585839,"identity":"efc89bd4-cb5f-4fb8-9d00-14df6b12170c","added_by":"auto","created_at":"2025-10-28 18:16:27","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":728520,"visible":true,"origin":"","legend":"\u003cp\u003ePredicted binding interactions between LuxR (cyan cartoon) and docked octylbenzene (orange sticks). Interacting residues (yellow sticks) within 5 Å include Tyr40, Tyr62, Pro63, Glu64, Trp66, and Ser116. Image generated in PyMOL.\u003c/p\u003e","description":"","filename":"luxrdockingfinal.png","url":"https://assets-eu.researchsquare.com/files/rs-7942069/v1/9303ca52276aa460f79c0176.png"},{"id":94595859,"identity":"505ba9d0-102b-42a3-9b17-3f30b1dfefc2","added_by":"auto","created_at":"2025-10-28 18:36:32","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1079260,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7942069/v1/5c5f3f8f-9691-4137-b090-ef5f87473f26.pdf"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003eMolecular docking analysis of LuxR with Octylbenzene\u003c/p\u003e","fulltext":[{"header":"1. Background","content":"\u003cp\u003eQuorum sensing (QS) is a cell-density dependent communication mechanism in bacteria that enables coordinated expression of genes involved in functions like virulence, biofilm formation, and motility [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. In Gram-negative bacteria, this communication relies on small diffusible molecules called acyl-homoserine lactones (AHLs) [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. LuxR-type transcriptional regulators are key components of this system, binding AHLs to initiate QS gene activation [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e]. Targeting LuxR with synthetic or non-canonical ligands provides a strategy to interfere with bacterial communication, offering alternatives to antibiotics [\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. Octylbenzene is a hydrophobic aromatic molecule with potential to mimic the nonpolar tail of long-chain AHLs [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. Hydrophobic AHL mimics are of interest because they may exhibit greater environmental stability and resist enzymatic degradation, making them promising leads for anti-virulence therapies against quorum-sensing-dependent pathogens [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. Therefore, it is of interest to report the Molecular docking analysis of LuxR with Octylbenzene.\u003c/p\u003e"},{"header":"2. Materials and Methods","content":"\u003ch4\u003e2.1. Ligand Selection and Properties\u003c/h4\u003e\n\u003cp\u003eOctylbenzene (CID: 16607) was selected from PubChem due to its hydrophobic, linear tail-like structure resembling long-chain AHLs. Its molecular weight is 198.3 g/mol, chemical formula C₁₄H₂₂, and logP is approximately 5.7. The SMILES notation is \u0026quot;CCCCCCCC1=CC=CC=C1\u0026quot;. Its physicochemical profile suggests compatibility with nonpolar protein pockets \u003cstrong\u003e[5]\u003c/strong\u003e.\u003c/p\u003e\n\u003ch4\u003e2.2. Receptor Preparation\u003c/h4\u003e\n\u003cp\u003eThe LuxR receptor model was derived from a homology-based structure using PDB template \u003cstrong\u003e3QP5\u003c/strong\u003e [\u003cstrong\u003e7\u003c/strong\u003e]. The PDB structure was cleaned in PyMOL \u003cstrong\u003e[8]\u0026nbsp;\u003c/strong\u003eby removing water and non-standard residues. AutoDock Tools (v1.5.7) was used to prepare the receptor by adding polar hydrogens and computing Gasteiger charges. The final file was saved in .pdbqt format as luxr_clean.pdbqt.\u003c/p\u003e\n\u003ch4\u003e2.3. Ligand Preparation\u003c/h4\u003e\n\u003cp\u003eOctylbenzene was downloaded in .sdf format from PubChem and converted to .pdbqt using Open Babel (v3.1.1). It was energy-minimized and hydrogens were added using AutoDock Tools \u003cstrong\u003e[5,8]\u003c/strong\u003e.\u003c/p\u003e\n\u003ch4\u003e2.4. Docking Protocol\u003c/h4\u003e\n\u003cp\u003eDocking was performed using AutoDock Vina (v1.1.2)\u003cstrong\u003e\u0026nbsp;[9]\u003c/strong\u003e with the following parameters:\u003c/p\u003e\n\u003cul\u003e\n \u003cli\u003eGrid center: X = \u0026ndash;3.793, Y = \u0026ndash;3.755, Z = 15.901\u003c/li\u003e\n \u003cli\u003eGrid size: 20 \u0026times; 20 \u0026times; 20 \u0026Aring;\u003c/li\u003e\n \u003cli\u003eExhaustiveness: default\u003c/li\u003e\n \u003cli\u003eCPUs used: 8\u003c/li\u003e\n \u003cli\u003eLigand: ahl.pdbqt\u003c/li\u003e\n \u003cli\u003eReceptor: luxr_clean.pdbqt\u003c/li\u003e\n \u003cli\u003eOutput: docked_luxr_ahl.pdbqt\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eThe docking log (vina_log.txt) showed successful convergence. The top-ranked pose had a binding affinity of \u0026ndash;3.0 kcal/mol with 0.0 \u0026Aring; RMSD, indicating a stable and unique interaction.\u003c/p\u003e\n\u003ch4\u003e2.5. Visualization and Interaction Analysis\u003c/h4\u003e\n\u003cp\u003eThe docking pose was visualized using PyMOL (v2.5). Residues within 5 \u0026Aring; were identified and labeled. 2D interaction diagrams were generated using Discovery Studio Visualizer 2021. Residue-level interaction annotations were based on chemical properties and spatial proximity.\u0026nbsp;\u003c/p\u003e"},{"header":"3. Results and Discussion","content":"\u003cp\u003eMolecular docking revealed a well-defined pose of octylbenzene (orange sticks) embedded within the hydrophobic pocket of LuxR (cyan cartoon) \u003cstrong\u003e(Figure 1).\u003c/strong\u003e The aromatic ring of Tyr40 aligns favorably with the ligand\u0026rsquo;s aromatic ring, suggesting \u0026pi;\u0026ndash;\u0026pi; stacking. Glu64, Lys65, and Ser116 appear to stabilize the ligand edges through polar or electrostatic interactions, while Trp66, Tyr62, and Pro63 form a hydrophobic shell around the ligand.\u003c/p\u003e\n\u003cp\u003eThe presence of multiple aromatic residues supports strong \u0026pi;\u0026ndash;\u0026pi; and van der Waals interactions. Glu115 and Ser116 contribute to conformational stabilization. Despite weaker binding (\u0026ndash;3.0 kcal/mol vs \u0026ndash;7.1 kcal/mol for AHL), octylbenzene docked in the same pocket, indicating potential competitive inhibition. \u0026nbsp; The findings indicate that hydrophobic molecules like octylbenzene can engage LuxR\u0026rsquo;s binding site in a manner comparable to native AHLs, supporting their use \u0026nbsp;as scaffolds for quorum-sensing inhibitor design.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTable 1. Predicted Residue\u0026ndash;Ligand Interactions in the LuxR\u0026ndash;Octylbenzene Complex\u003c/strong\u003e\u0026nbsp;\u003c/p\u003e\n\u003ctable border=\"1\" cellspacing=\"0\" cellpadding=\"0\" width=\"576\" class=\"fr-table-selection-hover\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eResidue\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eType\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eProperties\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eLikely Interaction\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eTYR40\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eAromatic\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003ePolar OH group + aromatic ring\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003e\u0026pi;\u0026ndash;\u0026pi; stacking, H-bond potential\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eASN61\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003ePolar\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eSide-chain amide\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003ePossible H-bond acceptor\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eTYR62\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eAromatic\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eAromatic + polar OH\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003e\u0026pi;\u0026ndash;\u0026pi; stacking / H-bond\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003ePRO63\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eNonpolar\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eAliphatic, rigid structure\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eVan der Waals\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eGLU64\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eCharged\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eAcidic (COO\u0026ndash;)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eElectrostatic (with polar atoms)\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eLYS65\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eCharged\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eBasic (NH₃⁺)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eMay stabilize ligand edge\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eTRP66\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eAromatic\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eHydrophobic + \u0026pi;-system\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eStrong \u0026pi;\u0026ndash;\u0026pi; or van der Waals\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eGLU115\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eCharged\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eAcidic\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eDistant stabilizer or steric limiter\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eSER116\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003ePolar\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eOH side chain\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eHydrogen bond donor\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eGLY117\u003c/p\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eNeutral\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eFlexible backbone\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 144px;\"\u003e\n \u003cp\u003eStructural support\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e\u003cem\u003eResidues were identified using spatial selection within 5 \u0026Aring; and analyzed using PyMOL.\u003c/em\u003e\u003c/p\u003e"},{"header":"4. Conclusion","content":"\u003cp\u003eThe interaction of LuxR with octylbenzene, a non-canonical, hydrophobic ligand is described. Docking analysis revealed stable binding involving key residues such as Tyr62, Trp66, Glu64, and Ser116. The pose resembled known AHL\u0026ndash;LuxR interactions, indicating that hydrophobic AHL mimics could act as quorum-sensing inhibitors. Although the predicted binding affinity is moderate, such ligands may still competitively occupy the binding site, warranting further validation through molecular dynamics simulations and in vitro assays.\u003c/p\u003e"},{"header":"Limitations","content":"\u003cp\u003eThis study is limited to in silico docking analysis. While docking scores provide an initial estimate of binding potential, further validation through molecular dynamics simulations and biochemical assays is required to confirm functional inhibition of LuxR.\u003c/p\u003e"},{"header":"Declarations","content":"\u003ch2\u003eEthical Compliance\u003c/h2\u003e\n\u003cp\u003eThis work adheres to the ethical guidelines of ICAR\u0026ndash;IARI, New Delhi. Institutional approval was obtained for the study.\u003c/p\u003e\n\u003ch2\u003eAcknowledgements\u003c/h2\u003e\n\u003cp\u003eThe authors would like to thank the Indian Agricultural Research Institute (ICAR\u0026ndash;IARI), New Delhi, for providing access to computational facilities and support during this study. We are grateful to Dr. Anupama Singh, Joint Director (Education), ICAR\u0026ndash;IARI, for guidance on ethical compliance. The authors acknowledges support from the institutional library resources for literature access. The authors also thank their colleagues for valuable discussions and technical assistance in molecular docking and visualization.\u003c/p\u003e\n\u003ch2\u003eData Availability\u003c/h2\u003e\n\u003cp\u003eAll data, scripts, and figure files used in this study are publicly available at the following GitHub repository:\u003c/p\u003e\n\u003cp\u003e\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/pankaj357/LuxR_Docking_Project\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eWhitehead NA et al. FEMS Microbiol Rev. 2001 25:365 [PMID:11524130].\u003c/li\u003e\n\u003cli\u003eVannini A et al. EMBO J. 2002 21:4393 [PMID:12198141].\u003c/li\u003e\n\u003cli\u003eGalloway WRJD et al. Chem Rev. 2011 111:28 [PMID:21182299].\u003c/li\u003e\n\u003cli\u003eHentzer M et al. EMBO J. 2003 22:3803 [PMID:12881415].\u003c/li\u003e\n\u003cli\u003ePubChem. Compound Summary for CID 16607, Octylbenzene. https://pubchem.ncbi.nlm.nih.gov/compound/16607\u003c/li\u003e\n\u003cli\u003eKalia VC. Biotechnol Adv. 2013 31:224 [PMID:23142623].\u003c/li\u003e\n\u003cli\u003eBerman HM et al. Nucleic Acids Res. 2000 28:235 [PMID:10592235].\u003c/li\u003e\n\u003cli\u003eSchr\u0026ouml;dinger LLC. PyMOL Molecular Graphics System, v2.5. 2021. https://pymol.org\u003c/li\u003e\n\u003cli\u003eTrott O \u0026amp; Olson AJ. J Comput Chem. 2010 31:455 [PMID:19499576].\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"Indian Agricultural Research Institute","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"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":"LuxR, quorum sensing, docking, AutoDock Vina, hydrophobic ligand, octylbenzene, PyMOL, AHL mimic","lastPublishedDoi":"10.21203/rs.3.rs-7942069/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7942069/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eLuxR-type transcriptional regulators mediate quorum sensing (QS) in Gram-negative bacteria by binding acyl-homoserine lactones (AHLs). Therefore, it is of interest to describe the molecular docking analysis of LuxR with octylbenzene (CID:16607), a non-natural hydrophobic ligand.\u003c/p\u003e\u003cp\u003eAutoDock Vina predicted a stable pose (\u0026ndash;3.0 kcal/mol) involving Tyr62, Trp66, and Glu64, while native AHL docking showed stronger affinity (\u0026ndash;7.1 kcal/mol). Despite its moderate affinity, octylbenzene occupied a similar binding pocket, highlighting hydrophobic scaffolds as potential quorum-sensing inhibitors.\u003c/p\u003e","manuscriptTitle":"Molecular docking analysis of LuxR with Octylbenzene","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-10-28 16:34:23","doi":"10.21203/rs.3.rs-7942069/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":"c7be1e2d-6be4-45f7-a46e-5a9519e90cce","owner":[],"postedDate":"October 28th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":56842095,"name":"Bioinformatics"}],"tags":[],"updatedAt":"2025-10-28T16:34:23+00:00","versionOfRecord":[],"versionCreatedAt":"2025-10-28 16:34:23","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7942069","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7942069","identity":"rs-7942069","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}