Skip to main content

Molecular Docking, Molecular Dynamics Simulations, Computational Screening to Design Quorum Sensing Inhibitors Targeting LuxP of Vibrio harveyi and Its Biological Evaluation


Quorum sensing (QS) plays an important role in the biofilm formation, production of virulence factors and stress responses in Vibrio harveyi. Therefore, interrupting QS is a possible approach to modulate bacterial behavior. In the present study, three docking protocols, such as Rigid Receptor Docking (RRD), Induced Fit Docking (IFD), and Quantum Polarized Ligand Docking (QPLD) were used to elucidate the binding mode of boronic acid derivatives into the binding pocket of LuxP protein in V. harveyi. Among the three docking protocols, IFD accurately predicted the correct binding mode of the studied inhibitors. Molecular dynamics (MD) simulations of the protein-ligand complexes indicates that the inter-molecular hydrogen bonds formed between the protein and ligand complex remains stable during the simulation time. Pharmacophore and shape-based virtual screening were performed to find selective and potent compounds from ChemBridge database. Five hit compounds were selected and subjected to IFD and MD simulations to validate the binding mode. In addition, enrichment calculation was performed to discriminate and separate active compounds from the inactive compounds. Based on the computational studies, the potent Bicyclo [2.2.1] hept-5-ene-2,3-dicarboxylic acid-2,6-dimethylpyridine 1-oxide (ChemBridge_5144368) was selected for in vitro assays. The compound exhibited dose dependent inhibition in bioluminescence and also inhibits biofilm formation in V. harveyi to the level of 64.25 %. The result from the study suggests that ChemBridge_5144368 could serve as an anti-quorum sensing molecule for V. harveyi.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12


  1. 1.

    Liu, P., Gao, Y., Huang, W., Shao, Z., Shi, J., & Liu, Z. (2012). A novel bioassay for high-throughput screening microorganisms with N-acyl homoserine lactone degradint activity. Applied Biochemistry and Biotechnology, 167, 73–80.

    CAS  Article  Google Scholar 

  2. 2.

    Vyshnava, S. S., Kander, D. K., Panjala, S. P., Pandian, K., Bontha, R. R., Goukanapalle, P. K., & Banganapalli, B. (2016). Effect of silver nanoparticles against the formation of biofilm by Pseudomonas aeruginosa an in silico approach. Applied Biochemistry and Biotechnology. doi:10.1007/s12010-016-2107-7.

    Google Scholar 

  3. 3.

    Federle, M. J. (2009). Autoinducer-2-based chemical communication in bacteria: complexities of interspecies signaling. Contributions to Microbiology, 16, 18–32.

    CAS  Article  Google Scholar 

  4. 4.

    Atkinson, S., & Williams, P. (2009). Quorum sensing and social networking in the microbial world. Journal of the Royal Soceity Interface, 6, 959–978.

    CAS  Article  Google Scholar 

  5. 5.

    Moran-Zorzano, M. T., Montero, M., Munoz, F. J., Alonso-Casajus, N., Viale, A. M., Eydallin, G., Sesma, M. T., Baroja-Fernandez, E., & Pozueta-Romero, J. (2008). Cytoplasmic Escherichia coli ADP sugar pyrophosphatase binds to cell membranes in response to extracellular signals as the cell population density increases. FEMS Microbiology Letters, 288, 25–32.

    CAS  Article  Google Scholar 

  6. 6.

    Rutherford, S. T., & Bassler, B. L. (2012). Bacterial quorum sensing: its role in virulence and possibilities for its control. Cold Spring Harbor Perspectives in Medicine, 2, a012427.

    Article  Google Scholar 

  7. 7.

    Sifri, C. D. (2008). Quorum sensing: bacteria talk sense. Healthcare Epidemiology, 47, 1070–1076.

    CAS  Google Scholar 

  8. 8.

    Roux, A., Payne, S. M., & Gilmore, M. S. (2009). Microbial telesensing: probing the environment for friends, foes, and food. Cell Host & Microbe, 6, 115–124.

    CAS  Article  Google Scholar 

  9. 9.

    Hentzer, M., & Givskov, M. (2003). Pharmacological inhibition of quorum sensing for the treatment of chronic bacterial infections. Journal of Clinical Investigation, 112, 1300–1307.

    CAS  Article  Google Scholar 

  10. 10.

    Bassler, B. L. (2002). Small talk: cell to cell communication in bacteria. Cell, 109, 421–424.

    CAS  Article  Google Scholar 

  11. 11.

    Schauder, S., Shokat, K., Surette, M. G., & Bassler, B. L. (2001). The LuxS family of bacterial autoinducers: biosynthesis of a novel quorum sensing signal molecule. Molecular Microbiology, 41, 463–476.

    CAS  Article  Google Scholar 

  12. 12.

    Neiditch, M. B., Federie, M. J., Miller, S. T., Bassler, B. L., & Hughson, F. M. (2005). Regulation of LuxPQ receptor activity by the quorum sensing signal autoinducer-2. Molecular Cell, 18, 507–518.

    CAS  Article  Google Scholar 

  13. 13.

    Chu, Y. Y., Nega, M., Wolfle, M., Plener, L., Grond, S., Jung, K., & Gotz, F. (2013). A new class of quorum quenching molecules from Staphylococcus species affects communication and growth of gram negative bacteria. PLoS Pathogens, 9, 1–14.

    Article  Google Scholar 

  14. 14.

    Waters, C., & Bassler, B. L. (2005). Quorum sensing: cell to cell communication in bacteria. Annual Review of Cell and Developmental Biology, 21, 319–346.

    CAS  Article  Google Scholar 

  15. 15.

    Neiditch, M. B., Federle, M. J., Pompeani, A. J., Kelly, R. C., Swem, D. L., Jeffrey, P. D., Bassler, B. L., & Hughson, F. M. (2006). Ligand induced asymmetry in histidine sensor kinase complex regulates quorum sensing. Cell, 126, 1095–1108.

    CAS  Article  Google Scholar 

  16. 16.

    Protein preparation wizard; Epik version 2.8 (2014) Schrödinger, LLC, New York, NY.

  17. 17.

    Ligprep, version 2.9 (2014). Schrödinger, LLC, New York, NY.

  18. 18.

    Glide, version, 6.2 (2014). Schrödinger, LLC, New York, NY.

  19. 19.

    Induced fit docking protocol, Glide version 6.1 (2014). Schrödinger, LLC, New York, NY.

  20. 20.

    QM-polarized ligand docking protocol, Glide version 5.7 (2014). Schrödinger, LLC, New York, NY.

  21. 21.

    Cho, A. E., Guallar, V., Berne, B. J., & Friesner, R. (2005). Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. Journal of Computational Chemistry, 26, 915–931.

    CAS  Article  Google Scholar 

  22. 22.

    Maestro desmond interoperability tools, version 3.0 (2014) Schrödinger, New York, NY.

  23. 23.

    Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., & Jorgensen, W. L. (2001). Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calucations on peptides. Journal of Physical Chemistry B, 105, 6474–6487.

    CAS  Article  Google Scholar 

  24. 24.

    Jorgensen, W. L., & Madura, J. D. (1985). Temperature and size dependence for Monte Carlo simulations of TIP4P water. Molecular Physics, 56, 1381–1392.

    CAS  Article  Google Scholar 

  25. 25.

    Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: an N center-dot. Log (N) method for Ewald sums in large systems. Journal of Chemical Physics, 98, 10089–10092.

    CAS  Article  Google Scholar 

  26. 26.

    Dixon, S. L., Smondyrev, A. M., & Rao, S. N. (2006). PHASE: a novel approach to pharmacophore modeling and 3D database searching. Chemical Biology & Drug Design, 67, 37–372.

    Article  Google Scholar 

  27. 27.

    Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society, 118, 11225–11236.

    CAS  Article  Google Scholar 

  28. 28.

    Dixon, S., Smondyrev, A., Knoll, E. H., Rao, S. N., Shaw, D. E., & Friesner, R. A. (2006). PHASE: a new engine for pharmacophore perception, 3D-QSAR model development, and 3D database screening: 1. Methodology and preliminary results. Journal of Computer-Aided Molecular Design, 20, 647–671.

    CAS  Article  Google Scholar 

  29. 29.

    Qikprop, version 3.9 (2014) Schrödinger, LLC, New York, NY.

  30. 30.

    Jaguar, version 8.3 (2014). Schrödinger, LLC, New York.

  31. 31.

    Lee, C., Yang, W., & Parr, R. G. (1988). Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Physical Review B: Condensed Matter, 37, 785–789.

    CAS  Article  Google Scholar 

  32. 32.

    Becke, A. D. (1993). Density functional thermochemistry. III. The role of exact exchange. Journal of Chemical Physics, 98, 5648–5652.

    CAS  Article  Google Scholar 

  33. 33.

    Binkley, J. S., Pople, J. A., & Hehre, W. J. (1980). Self consistent molecular orbital methods. 21. Small split valence basis sets for first row elements. Journal of the American Chemical Society, 102, 939–947.

    CAS  Article  Google Scholar 

  34. 34.

    Prime, version 3.5 (2014). Schrödinger, LLC, New York, NY.

  35. 35.

    Musthafa, K. S., Saroja, V., Pandian, S. K., & Ravi, A. V. (2011). Antipathogenic potential of marine Bacillus sp. SS4 on N-acyl-homoserine-lactone-mediated virulence factors production in Pseudomonas aeruginosa (PAO1). Journal of Biosciences, 36, 55–67.

    CAS  Article  Google Scholar 

  36. 36.

    Jesudhasan, P. R., Cepeda, M. L., Widmer, K., Dowd, S. E., Soni, K. A., Hume, M. E., Zhu, J., & Pillai, S. D. (2010). Transcriptome analysis of genes controlled by luxS/autoinducer-2 in Salomonella enterica serovar Typhimurium. Foodborne Pathogens and Disease, 7, 399–410.

    CAS  Article  Google Scholar 

  37. 37.

    Ni, N., Chou, H. T., Wang, J., Li, M., Lu, C., Tai, P. C., & Wang, B. (2008). Identification of boronic acids as antagonists of bacterial quorum sensing in Vibrio harveyi. Biochemical and Biophysical Research Communication, 369, 590–594.

    CAS  Article  Google Scholar 

  38. 38.

    Wang, X., Pan, P., Li, Y., Li, D., & Hou, T. (2014). Exploring the prominent performance of CX-4945 derivatives as protein kinase CK2 inhibitors by a combined computation study. Molecular Biosystem, 10, 1196–1210.

    CAS  Article  Google Scholar 

  39. 39.

    Li, M., Ni, N., Chou, H. T., Lu, C. D., Tai, P. C., & Wang, B. (2008). Structure based discovery and experimental verification of novel AI-2 quorum sensing inhibitors against Vibrio harveyi. ChemMedChem, 3, 1242–1249.

    CAS  Article  Google Scholar 

  40. 40.

    Adcock, S. A., & McCammon, J. A. (2006). Molecular dynamics: survey of methods for simulating the activity of protein. Chemical Review, 106, 1589–1615.

    CAS  Article  Google Scholar 

  41. 41.

    Cardone, A., Hassan, S. A., Albers, R. W., Sriram, R. D., & Pant, H. C. (2010). Structural and dynamic determinants of ligand binding and regulation of cyclin-dependent kinase 5 by pathological activator p25 and inhibitory peptide CIP. Journal of Molecular Biology, 401, 478–492.

    CAS  Article  Google Scholar 

  42. 42.

    Cembran, A., Kim, J., Gao, J., & Gianluigi, V. (2014). NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding. Physical Chemistry Chemical Physics, 16, 6508–6518.

    CAS  Article  Google Scholar 

  43. 43.

    Ballone, P. (2014). Modeling potential energy surfaces: from first principle approaches to empirical force fields. Entropy, 16, 322–349.

    Article  Google Scholar 

  44. 44.

    Williams, M. A., & Ladbury, J. E. (2008). Hydrogen bonds in protein ligand complexes. Wiley-VCH Verlag GmbH & Co. KGaA. Protein science encyclopedia.

  45. 45.

    Reddy, K. K., Singh, S. K., Tripathi, S. K., Selvaraj, C., & Suryanarayanan, V. (2014). Shape and pharmacophore based virtual screening to identify potential cytochrome P450 sterol 14α-demethylase inhibitors. Journal of Receptor and Signal Transduction Research, 33, 234–243.

    Article  Google Scholar 

  46. 46.

    Johnson, E. R., Yang, W., & Davidson, E. R. (2010). Spin-state splittings, highest occupied molecular orbital and lowest unoccupied molecular orbital energies and chemical hardness. Journal of Chemical Physics, 133, 164107.

    Article  Google Scholar 

  47. 47.

    Genc, Z. K., Tkin, S., Sandal, S., Sekerci, M., & Genc, M. (2014). Synthesis and DFT studies of structural and some spectral parametes of nickel (II) complex with 2-(2-hydroxybenzoyl)-N-(1-adamantyl) hydrazine carbothioamide. Research on Chemical Intermediates, 41, 4477–4488.

    Article  Google Scholar 

  48. 48.

    Eroglu, E., Turkmen, H., Guler, S., Palaz, S., & Oltulu, O. (2007). A DFT based QSAR study of acetazolamide/sulfanilamide derivatives with carbonic anhydrase (CA-II) isozyme inhibitory activity. International Journal of Molecular Sciences, 8, 145–155.

    CAS  Article  Google Scholar 

  49. 49.

    Galloway, W. R., Hodgkinson, J. T., Bowden, S., Welch, M., & Spring, D. R. (2012). Applications of small molecule activators and inhibitors of quorum sensing in gram-negative bacteria. Trends in Microbiology, 9, 449–458.

    Article  Google Scholar 

  50. 50.

    Henke, J. M., & Bassler, B. L. (2004). Quorum sensing regulates type III secretion in Vibrio harveyi and Vibrio parahaemolyticus. Journal of Bacteriology, 186, 3794–3805.

    CAS  Article  Google Scholar 

  51. 51.

    Parvez, S., Venkataraman, C., & Mukherji, S. (2006). A review on advantages on implementing luminescence inhibition test (Vibrio fisheri) for acute toxicity prediction of chemicals. Environmental International, 32, 265–268.

    CAS  Article  Google Scholar 

  52. 52.

    Vikram, A., Jesudhasan, P. R., Jayaprakasha, G. K., Pillai, S. D., & Patil, B. S. (2011). Citrus limonids interfere with Vibrio harveyi cell-cell signalling and biofilm formation by modulating the response regulator LuxO. Microbiology, 157, 99–110.

    CAS  Article  Google Scholar 

  53. 53.

    Defoirdt, T., Crab, R., Wood, T. K., Sorgeloos, P., Verstraete, W., & Bossier, P. (2006). Quorum sensing disrupting brominated furanones protect the gnotobiotic brine shrimp Artemia franciscana from pathogenic Vibrio harveyi, Vibrio campbellii, and Vibrio parahaemolyticus isolates. Applied and Environmental Microbiology, 72, 6419–6423.

    CAS  Article  Google Scholar 

  54. 54.

    Huang, R., Li, M., & Gregory, R. L. (2011). Bacterial interactions in dental biofilm. Virulence, 25, 435–444.

    Article  Google Scholar 

  55. 55.

    Kadirvel, M., Fanimarvasti, F., Forbes, S., McBain, A., Gardiner, J. M., Brown, G. D., & Freeman, S. (2014). Inhibition of quorum sensing and biofilm formation in Vibrio harveyi by 4-fluoro-DPD; a novel potent inhibitor of signalling. Chemical Communications, 39, 5000–5002.

    Article  Google Scholar 

  56. 56.

    Janssens, J. C., Steenackers, H., Robijns, S., Gellens, E., Levin, J., Zhao, H., Hermans, K., De Coster, D., Verhoeven, T. L., Marchal, K., Vanderleyden, J., De Vos, D. E., & De Keersmaecker, S. C. (2008). Brominated furanones inhibit biofilm formation by Salmonella enteric serovar Typhimurium. Applied and Environmental Microbiology, 74, 6639–6648.

    CAS  Article  Google Scholar 

  57. 57.

    Ren, D., Bedzyk, L. A., Ye, R. W., Thomas, S. M., & Wood, T. K. (2004). Differential gene expression shows natural brominated furanones interfere with the autoinducer-2 bacterial signaling system of Escherichia coli. Biotechnolgy and Bioprocess Engineering, 88, 630–642.

    CAS  Google Scholar 

  58. 58.

    Ren, D., Sims, J. J., & Wood, T. K. (2002). Inhibition of biofilm formation and swarming of Bacillus subtilis by (5z)-4-bromo-5-(bromo-methylene)-3-butyl-2(5H)-furanone. Letters in Applied Microbiology, 34, 293–299.

    CAS  Article  Google Scholar 

  59. 59.

    He, Z., Wang, Q., Hu, Y., Liang, J., Jiang, Y., Ma, R., Tang, Z., & Huang, Z. (2012). Use of the quorum sensing inhibitor furanone C-30 to interfere with biofilm formation by Streptococcus mutans and its luxS mutant strain. International Journal of Antimicrobial Agents, 40, 30–35.

    Article  Google Scholar 

  60. 60.

    Lade, H., Paul, D., & Kweon, J. H. (2014). Quorum quenching mediated approaches for control of membrane biofouling. International Journal of Biological Sciences, 10, 550–565.

    Article  Google Scholar 

  61. 61.

    Davies, J., & Davies, D. (2010). Origins and evolution of antibiotic resistance. Microbiology and Molecular Biology Reviews, 74, 417–433.

    CAS  Article  Google Scholar 

  62. 62.

    Chow, S., Gu, K., Jiang, L., & Nassour, A. (2011). Salicylic acid affects swimming, twitching and swarming motility in Pseudomonas aeruginosa resulting in decreased biofilm formation. Journal of Experimental Microbiology and Immunology, 15, 22–29.

    Google Scholar 

  63. 63.

    Yildiz, F. H., & Visick, K. L. (2009). Vibrio biofilms: so much the same yet so different. Trends in Microbiology, 17, 109–118.

    CAS  Article  Google Scholar 

  64. 64.

    O’May, C., & Tufenkji, N. (2011). The swarming motility of Pseudomonas aeruginosa is blocked by cranberry proanthocyanidins and other tannin containing materials. Applied and Environmental Microbiology, 77, 3061–3067.

    Article  Google Scholar 

Download references

Author information



Corresponding author

Correspondence to Pappu Srinivasan.

Electronic supplementary material

Supplementary Fig. 1

The RMSD of C-α atom from the starting structure as the function of the simulation time (GIF 215 kb)

Supplementary Fig. 2

RMSF of C-α atom in coordinates of each residue averaged over the duration of the MD simulation (GIF 173 kb)

Supplementary Fig. 3

Hydrogen bonding number versus simulation time (GIF 25 kb)

Supplementary Fig. 4

Effect of ChemBridge_5144368 on biofilm formation of V. harveyi (GIF 10 kb)

High resolution image (TIFF 10443 kb)

High resolution image (TIFF 8975 kb)

High resolution image (TIFF 1484 kb)

High resolution image (TIFF 1224 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Rajamanikandan, S., Jeyakanthan, J. & Srinivasan, P. Molecular Docking, Molecular Dynamics Simulations, Computational Screening to Design Quorum Sensing Inhibitors Targeting LuxP of Vibrio harveyi and Its Biological Evaluation. Appl Biochem Biotechnol 181, 192–218 (2017).

Download citation


  • Quorum sensing
  • Boronic acid derivatives
  • Molecular docking
  • Molecular dynamics simulations
  • In vitro assays