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dc.contributor.advisorVivas Reyes, Ricardo (Director/a)
dc.contributor.advisorAlí Torres, Jorge Isaac (Director/a)
dc.contributor.advisorZapata Rivera, Jhon (Director/a)
dc.contributor.authorAhumedo Monterrosa, Maicol José
dc.date.accessioned2020-03-13T14:22:00Z
dc.date.available2020-03-13T14:22:00Z
dc.date.issued2018
dc.identifier.citationTD541.28 / A86es
dc.identifier.urihttps://hdl.handle.net/11227/10030
dc.identifier.urihttp://dx.doi.org/10.57799/11227/79
dc.descriptionTesis (Doctor en Ciencias). -- Universidad de Cartagena. Facultad de Ciencias Exactas y Naturales, 2018es
dc.description.abstractEn el presente trabajo, se realizó un estudio de modelado molecular que combina cálculos de acoplamiento molecular, relación cuantitativa estructura actividad 3D basado en el receptor, simulaciones de dinámica molecular y cálculos de energía libre de unión, sobre un conjunto de 28 análogos estructurales de las N-acil homoserina lactonas (AHLs) con actividad antagonista de Quorum sensing, con el propósito de comprender el modo de unión y el microambiente molecular al cual están expuestos los 28 análogos en el sitio activo del receptor LasR en Pseudomona aeruginosaes
dc.format.mediumapplication/pdf
dc.language.isospaes
dc.publisherUniversidad de Cartagenaes
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0
dc.subjectEstructura moleculares
dc.subjectQuímica cuánticaes
dc.subjectQuímicaes
dc.titleModelado molecular de análogos estructurales de las Acil homoserina lactonas en el sitio activo del receptor Lasres
dc.typeTrabajo de grado - Doctoradospa
dcterms.referencesAbagyan, R., Totrov, M., & Kuznetsov, D. (1994). New Method for Protein Modeling and Design : Applications to Docking and Structure Prediction from the Distorted Native Conformation. Journal of Computational Chemistry, 15(5), 488–506.
dcterms.referencesAdcock, S. A., & McCammon, J. A. (2006). Molecular dynamics: Survey of methods for simulating the activity of proteins. Chemical Reviews, 106(5), 1589–1615. https://doi.org/10.1021/cr040426m
dcterms.referencesAhlgren, N. a, Harwood, C. S., Schaefer, A. L., Giraud, E., & Greenberg, E. P. (2011). Aryl-homoserine lactone quorum sensing in stem-nodulating photosynthetic bradyrhizobia. Proceedings of the National Academy of Sciences of the United States of America, 108(17), 7183–7188. https://doi.org/10.1073/pnas.1103821108
dcterms.referencesAhumedo, M., Díaz, A., & Vivas-Reyes, R. (2010). Theoretical and structural analysis of the active site of the transcriptional regulators LasR and TraR, using molecular docking methodology for identifying potential analogues of acyl homoserine lactones (AHLs) with anti-quorum sensing activity. European Journal of Medicinal Chemistry, 45(2), 608–615. https://doi.org/10.1016/j.ejmech.2009.11.004
dcterms.referencesAhumedo, M., Drosos, J. C., & Vivas-Reyes, R. (2014a). Application of molecular docking and ONIOM methods for the description of interactions between anti-quorum sensing active (AHL) analogues and the Pseudomonas aeruginosa LasR binding site. Molecular bioSystems, 10(5), 1162–71. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/24626770
dcterms.referencesAhumedo, M., Drosos, J. C., & Vivas-Reyes, R. (2014b). Application of molecular docking and ONIOM methods for the description of interactions between anti-quorum sensing active (AHL) analogues and the Pseudomonas aeruginosa LasR binding site. Molecular bioSystems, 10(5), 1162–71. https://doi.org/10.1039/c3mb70181f
dcterms.referencesAlberto, G., & Rossello, M. (2013). Quorum sensing en bacterias y levaduras. Medicina Clinica, 141(8), 353–357.
dcterms.referencesAmara, N., Mashiach, R., Amar, D., Krief, P., Spieser, A. H., Bottomley, M. J., … Meijler, M. M. (2009). Covalent Inhibition of Bacterial Quorum Sensing, (8), 197–201. https://doi.org/10.1002/cbic.201500676
dcterms.referencesAtkinson, S., & Williams, P. (2009). Quorum sensing and social networking in the microbial world. Journal of the Royal Society, Interface / the Royal Society, 6(40), 959–78. https://doi.org/10.1098/rsif.2009.0203
dcterms.referencesAuffinger, P., Hays, F. A., Westhof, E., & Ho, P. S. (2004). Halogen bonds in biological molecules. Proc. Natl. Acad. Sci., 101(48), 16789–16794.
dcterms.referencesBai, A. J., & Rai, V. R. (2011). Bacterial Quorum Sensing and Food Industry. Comprehensive Reviews in Food Science and Food Safety, 10(3), 183– 193. https://doi.org/10.1111/j.1541-4337.2011.00150.x
dcterms.referencesBassler, B. L., & Losick, R. (2006). Bacterially Speaking. Cell, 125(2), 237–246. https://doi.org/10.1016/j.cell.2006.04.001
dcterms.referencesBassler, B. L., & Ng, W. (2009). NIH Public Access. Annu. Rev. Genet, 43, 197– 222. https://doi.org/10.1146/annurev-genet-102108-134304.Bacterial
dcterms.referencesBayly, C. C. I., Cieplak, P., Cornell, W. D., & Kollman, P. a. (1993). A wellbehaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. The Journal of Physical …, 97, 10269–10280. https://doi.org/10.1021/j100142a004
dcterms.referencesBhargava, N., Sharma, P., & Capalash, N. (2010). Quorum sensing in Acinetobacter : an emerging pathogen, 36(July), 349–360. https://doi.org/10.3109/1040841X.2010.512269
dcterms.referencesBlackwell, H. E., & Fuqua, C. (2011). Introduction to bacterial signals and chemical communication. Chemical Reviews, 111(1), 1–3. https://doi.org/10.1021/cr100407j
dcterms.referencesBlankenship, J. R., & Mitchell, A. P. (2006). How to build a biofilm: a fungal perspective. Current Opinion in Microbiology, 9(6), 588–594. https://doi.org/10.1016/j.mib.2006.10.003
dcterms.referencesBonomo, R. A., & Szabo, D. (2006). Mechanisms of Multidrug Resistance in Acinetobacter Species and Pseudomonas aeruginosa. Clinical Infectious Diseases, 44106, 49–56.
dcterms.referencesBottomley, M. J., Muraglia, E., Bazzo, R., & Carfì, A. (2007). Molecular insights into quorum sensing in the human pathogen Pseudomonas aeruginosa from the structure of the virulence regulator LasR bound to its autoinducer. Journal of Biological Chemistry, 282(18), 13592–13600. https://doi.org/10.1074/jbc.M700556200
dcterms.referencesBoucher, H. W., Talbot, G. H., Benjamin, D. K., Bradley, J., Guidos, R. J., Jones, R. N., … Gilbert, D. (2013). 10 x ’20 Progress--development of new drugs active against gram-negative bacilli: an update from the Infectious Diseases Society of America. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America, 56(12), 1685–94. https://doi.org/10.1093/cid/cit152
dcterms.referencesBrown, S. A., Palmer, K. L., & Whiteley, M. (2008). Revisiting the host as a growth medium. MICROBIOLOGY, 6, 657–666. https://doi.org/10.1038/nrmicro1955
dcterms.referencesBurton, E. O., Read, H. W., Pellitteri, M. C., & Hickey, W. J. (2005). Identification of acyl-homoserine lactone signal molecules produced by Nitrosomonas europaea strain Schmidt. Applied and Environmental Microbiology, 71(8), 4906–4909. https://doi.org/10.1128/AEM.71.8.4906- 4909.2005
dcterms.referencesCai, W., Li, J., & Yip, S. (2012). Molecular Dynamics. Comprehensive Nuclear Materials, 1, 249–265. https://doi.org/10.1016/B978-0-08-056033-5.00128- 2
dcterms.referencesCamilli, A., & Bassler, B. . (2006). NIH Public Access. Nature Reviews. Microbiology, 311(5764), 1113–1116. https://doi.org/10.1126/science.1121357.Bacterial
dcterms.referencesCavasotto, C. (2016). In Silico drug Discovery and Design Theory, Methods, Challenges, and Applications.
dcterms.referencesCegelski, L., Marshall, G. R., Eldridge, G. R., & Hultgren, S. J. (2008). NIH Public Access. Nat Rev Microbiol, 6(1), 17–27.
dcterms.referencesCereto-Massagué, A., Ojeda, M. J., Valls, C., Mulero, M., Garcia-Vallvé, S., & Pujadas, G. (2015). Molecular fingerprint similarity search in virtual screening. Methods, 71(C), 58–63. https://doi.org/10.1016/j.ymeth.2014.08.005
dcterms.referencesChakrabarti, S., & Sowdhamini, R. (2003). Functional sites and evolutionary connections of acylhomoserine lactone synthases. Protein Engineering, 16(4), 271–278. https://doi.org/DOI 10.1093/proeng/gzg031
dcterms.referencesChen, G., Swem, L. R., Swem, D. L., Stauff, D. L., O'Loughlin, C. T., Jeffrey, P. D., … Hughson, F. M. (2011). A Strategy for Antagonizing Quorum Sensing. Molecular Cell, 42(2), 199–209. https://doi.org/10.1016/j.molcel.2011.04.003
dcterms.referencesCheng, T., Li, Q., Zhou, Z., Wang, Y., & Bryant, S. H. (2012). Structure-based virtual screening for drug discovery: a problem-centric review. The AAPS Journal, 14(1), 133–41. https://doi.org/10.1208/s12248-012-9322-0
dcterms.referencesChipot, C. (2014). Frontiers in free-energy calculations of biological systems. Computational Molecular Science, 4(1), 71– 89. https://doi.org/10.1002/wcms.1157
dcterms.referencesCho, T., Nagao, J., Imayoshi, R., Kaminishi, H., Aoyama, T., & Nakayama, H. (2010). Quorum Sensing and Morphological Regulation in the Pathogenic Fungus Candida albicans. Journal of Oral Biosciences, 52(3), 233–239. https://doi.org/10.1016/S1349-0079(10)80026-X
dcterms.referencesChristensen, Q. H., Brecht, R. M., Dudekula, D., Greenberg, E. P., & Nagarajan, R. (2014). Evolution of Acyl-Substrate Recognition by a Family of AcylHomoserine Lactone Synthases. PLoS ONE, 9(11), 1–8. https://doi.org/10.1371/journal.pone.0112464
dcterms.referencesChurchill, M. E. A., & Chen, L. (2011). NIH Public Access (Vol. 111). https://doi.org/10.1021/cr1000817.Structural
dcterms.referencesCramer, C. J. (2004). Essentials of Computational Chemistry Theories and Models. New York (Second Edi). https://doi.org/10.1037/023990
dcterms.referencesCramer, R. D., Patterson, D. E., & Bunce, J. D. (1988). Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc, 110(12), 5959–5967.
dcterms.referencesCrousilles, A., Maunders, E., Bartlett, S., Fan, C., Abdelhamid, Y., Baker, Y., … Welch, M. (2015). Which microbial factors really are important in Pseudomonas aeruginosa infections ? Future Microbiology, 10(11), 1825– 1836.
dcterms.referencesCuevas, G., & Cortés, F. (2003). Introducción a la Química Computacional.
dcterms.referencesDanishuddin, M., & Khan, A. U. (2015). Structure based virtual screening to discover putative drug candidates: Necessary considerations and successful case studies. Methods, 71(C), 135–145. https://doi.org/10.1016/j.ymeth.2014.10.019
dcterms.referencesde Souza, O. N., & Ornstein, R. L. (1997). Effect of periodic box size on aqueous molecular dynamics simulation of a DNA dodecamer with particlemesh Ewald method. Biophysical Journal, 72(6), 2395–7. https://doi.org/10.1016/S0006-3495(97)78884-2
dcterms.referencesDekimpe, V., & Déziel, E. (2009). Revisiting the quorum-sensing hierarchy in Pseudomonas aeruginosa : the transcriptional regulator RhlR regulates LasR-specific factors. Microbiology, 155, 712–723. https://doi.org/10.1099/mic.0.022764-0
dcterms.referencesDennington, R., Keith, T., & Millam, J. (2009). GaussView. Semichem Inc., Shawnee Mission KS.
dcterms.referencesDong, Y., Xu, J., Li, X., & Zhang, L. (2000). AiiA , an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of Erwinia carotovora. Proc. Natl. Acad. Sci, 97(7), 3526–3531.
dcterms.referencesDonlan, R. M., & Costerton, J. W. (2002). Biofilms : Survival Mechanisms of Clinically Relevant Microorganisms. CLINICAL MICROBIOLOGY REVIEWS, 15(2), 167–193. https://doi.org/10.1128/CMR.15.2.167
dcterms.referencesDoshi, H. K., Chua, K., Kagda, F., & Tambyah, P. A. (2011). Multi drug resistant pseudomonas infection in open fractures post definitive fixation leading to limb loss : A report of three cases. International Journal of Case Reports and Images, 2(5), 1–6. https://doi.org/10.5348/ijcri-2011-05-31-CS-1
dcterms.referencesDuan, Y., Wu, C., Chowdhury, S. S., Lee, M. C., Xiong, G., Zhang, W., … Kollman, P. (2003). A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry, 24(16), 1999–2012. https://doi.org/10.1002/jcc.10349
dcterms.referencesEberhard, C., Dew, W., Science, D. R., Eberhard, A., Burlingame, A. L., Kenyon, G. L., … Oppenheimer, N. J. (1981). Structural Identification of Autoinducer of Photobacterium fischeri. Biochemistry 1981, 20, 2444– 2449.
dcterms.referencesFolkesson, A., Jelsbak, L., Yang, L., Johansen, H. K., Ciofu, O., Høiby, N., & Molin, S. (2012). Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway : an evolutionary perspective. Nature Reviews Microbiology, 10(12), 841–851. https://doi.org/10.1038/nrmicro2907
dcterms.referencesFrei, R., Breitbach, A. S., & Blackwell, H. E. (2012). 2-Aminobenzimidazole Derivatives Strongly Inhibit and Disperse Pseudomonas aeruginosa Biofilms ** Angewandte. Angew. Chem. Int, (51), 1–5. https://doi.org/10.1002/anie.201109258
dcterms.referencesFriesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., … Shenkin, P. S. (2004). Glide : A New Approach for Rapid , Accurate Docking and Scoring . 1 . Method and Assessment of Docking Accuracy. J. Med. Chem, 47(7), 1739–1749.
dcterms.referencesFrisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A. et al. (2009). Gaussian 09. Wallingford: Gaussian, Inc.
dcterms.referencesFrisch, J. B., & Foresman, A. (1994). Exploring_Chemistry_With_Electronic_Structure_Methods.
dcterms.referencesFuqua, C., & Greenberg, E. P. (2002). Listening in on bacteria: acyl-homoserine lactone signalling. Nature Reviews in Molecular Cell Biology, 3(September), 685–695. https://doi.org/10.1038/nrm907
dcterms.referencesFuqua, W. C., Winans, S. C., & Greenberg, E. P. (1994). Quorum sensing in bacteria: The LuxR-LuxI family of cell density- responsive transcriptional regulators. Journal of Bacteriology, 176(2), 269–275. https://doi.org/10.1111/j.1462-5822.2006.00734.x
dcterms.referencesGalloway, W. R. J. D., Hodgkinson, J. T., Bowden, S. D., Welch, M., & Spring, D. R. (2011). Quorum sensing in Gram-negative bacteria: Small-molecule modulation of AHL and AI-2 quorum sensing pathways. Chemical Reviews, 111(1), 28–67. https://doi.org/10.1021/cr100109t
dcterms.referencesGalloway, W. R. J. D., 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, 20(9), 449–458. https://doi.org/10.1016/j.tim.2012.06.003
dcterms.referencesGenheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 441(October), 1–13. https://doi.org/10.1517/17460441.2015.1032936
dcterms.referencesGerdt, J. P., McInnis, C. E., Schell, T. L., & Blackwell, H. E. (2015). Unraveling the contributions of hydrogen-bonding interactions to the activity of native and non-native ligands in the quorum-sensing receptor LasR. Org. Biomol. Chem., 13, 1453–1462. https://doi.org/10.1039/C4OB02252A
dcterms.referencesGerdt, J. P., McInnis, C. E., Schell, T. L., Rossi, F. M., & Blackwell, H. E. (2014a). Mutational analysis of the quorum-sensing receptor LasR reveals interactions that govern activation and inhibition by nonlactone ligands. Chemistry and Biology, 21(10), 1361–1369. https://doi.org/10.1016/j.chembiol.2014.08.008
dcterms.referencesGerdt, J. P., McInnis, C. E., Schell, T. L., Rossi, F. M., & Blackwell, H. E. (2014b). Mutational analysis of the quorum-sensing receptor LasR reveals interactions that govern activation and inhibition by nonlactone ligands. Chemistry and Biology, 21(10), 1361–1369. https://doi.org/10.1016/j.chembiol.2014.08.008
dcterms.referencesGeske, G. D., Mattmann, M. E., & Blackwell, H. E. (2008). Evaluation of a focused library of N-aryl l-homoserine lactones reveals a new set of potent quorum sensing modulators. Bioorganic and Medicinal Chemistry Letters, 18(22), 5978–5981. https://doi.org/10.1016/j.bmcl.2008.07.089
dcterms.referencesGeske, G. D., Neill, J. C. O., & Blackwell, H. E. (2008). NIH Public Access, 37(7), 1432–1447. https://doi.org/10.1039/b703021p.Expanding
dcterms.referencesGeske, G. D., O’Neill, J. C., Miller, D. M., Mattmann, M. E., & Blackwell, H. E. (2007). Modulation of Bacterial Quorum Sensing with Synthetic Ligands: Systematic Evaluation of N -Acylated Homoserine Lactones in Multiple Species and New Insights into Their Mechanisms of Action. Journal of the American Chemical Society, 129(44), 13613–13625. https://doi.org/10.1021/ja074135h
dcterms.referencesGodbout, N., Salahub, D. R., Andzelm, J., & Wimmer, E. (1992). Optimization of Gaussian-type basis sets for local spin density functional calculations. Part I. Boron through neon, optimization technique and validation. Canadian Journal of Chemistry, 70(2), 560–571. https://doi.org/10.1139/v92-079
dcterms.referencesGonzález, J. E., & Marketon, M. M. (2003). Quorum sensing in nitrogen-fixing rhizobia. Microbiology and Molecular Biology Reviews : MMBR, 67(4), 574– 92. https://doi.org/10.1128/MMBR.67.4.574
dcterms.referencesGoodisman, J. (1973). Diatomic interaction potential theory. Academic Press, 1.
dcterms.referencesGould, T., Schweizer, H., & Churchill, M. (2004). Structure of the Pseudomonas aeruginosa acyl- homoserinelactone synthase LasI. Molecular Microbiology (2004), 53(4), 1135–1146. https://doi.org/10.1111/j.1365- 2958.2004.04211.x
dcterms.referencesGutiérres-de-Terán, H. (2004). Modelización molecular de los receptores de adenosina y sus ligandos en el marco de diseño de fármacos asistido por ordenador, 28–29. Retrieved from http://hdl.handle.net/10230/11902
dcterms.referencesHanzelka, B. L., & Greenberg, E. P. (1996). Quorum sensing in Vibrio fischeri : evidence that S-adenosylmethionine is the amino acid substrate for autoinducer synthesis . Quorum Sensing in Vibrio fischeri : Evidence that S -Adenosylmethionine Is the Amino Acid Substrate for Autoinducer Synthesis. Journal of Bacteriology, 178(17), 5291–5294.
dcterms.referencesHartmann, A., & Schikora, A. (2012). Quorum Sensing of Bacteria and TransKingdom Interactions of N -Acyl Homoserine Lactones with Eukaryotes. J Chem Ecol, 38(6), 704–713. https://doi.org/10.1007/s10886-012-0141-7
dcterms.referencesHenke, J. M., & Bassler, B. L. (2004). Bacterial social engagements. Trends in Cell Biology, 14(11), 648–656. https://doi.org/10.1016/j.tcb.2004.09.012
dcterms.referencesHense, B. A., & Schuster, M. (2015). Core principles of bacterial autoinducer systems. Microbiology and Molecular Biology Reviews : MMBR, 79(1), 153–69. https://doi.org/10.1128/MMBR.00024-14
dcterms.referencesHentzer, M., & Givskov, M. (2003). Pharmacological inhibition of quorum sensing for the treatment of chronic bacterial infections. J. Clin. Invest., 112(9), 1300–1307. https://doi.org/10.1172/JCI200320074.One
dcterms.referencesHentzer, M., Riedel, K., Rasmussen, T. B., Heydorn, A., Andersen, J. B., Parsek, M. R., … Givskov, M. (2002). Inhibition of quorum sensing in Pseudomonas aeruginosa biofilm bacteria by a halogenated furanone compound. Microbiology, 148, 87–102.
dcterms.referencesHETÉNYI, C., & VAN DER SPOEL, D. (2002). Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Science (2002), 11, 1729–1737. https://doi.org/10.1110/ps.0202302.the
dcterms.referencesHomeyer, N., & Gohlke, H. (2012). Free Energy Calculations by the Molecular Mechanics Poisson-Boltzmann Surface Area Method. Molecular Informatics, 31, 114–122. https://doi.org/10.1002/minf.201100135
dcterms.referencesHomeyer, N., & Gohlke, H. (2013). Advances in molecular dynamics simulations and free-energy calculations relevant for drug design. In M. A. Lill (Ed.), In Silico Drug Discovery and Design (pp. 51–64).
dcterms.referencesHuang, J. J., Han, J., Zhang, L., & Leadbetter, J. R. (2003). Utilization of AcylHomoserine Lactone Quorum Signals for Growth by a Soil Pseudomonad and Pseudomonas aeruginosa PAO1. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 69(10), 5941–5949. https://doi.org/10.1128/AEM.69.10.5941
dcterms.referencesHuang, J., Shi, Y., Zeng, G., Gu, Y., & Chen, G. (2016). Acyl-homoserine lactone-based quorum sensing and quorum quenching hold promise to determine the performance of biological wastewater treatments : An overview. Chemosphere, 157, 137–151. https://doi.org/10.1016/j.chemosphere.2016.05.032
dcterms.referencesHuang, S. Y., & Zou, X. (2010). Advances and challenges in Protein-ligand docking. International Journal of Molecular Sciences, 11(8), 3016–3034. https://doi.org/10.3390/ijms11083016
dcterms.referencesHudaiberdiev, S., Choudhary, K. S., Vera Alvarez, R., Gelencsér, Z., Ligeti, B., Lamba, D., & Pongor, S. (2015). Census of solo LuxR genes in prokaryotic genomes. Frontiers in Cellular and Infection Microbiology, 5(March), 20. https://doi.org/10.3389/fcimb.2015.00020
dcterms.referencesHumphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics. https://doi.org/10.1016/0263- 7855(96)00018-5
dcterms.referencesJensen, F. (2007). Introduction to Computational Chemistry Computational Chemistry.
dcterms.referencesJones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997). Development and Validation of a Genetic Algorithm for Flexible Docking. Journal of Molecular Biology, 267(3), 727–748.
dcterms.referencesJorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926. https://doi.org/10.1063/1.445869
dcterms.referencesKalia, V. C., & Purohit, H. J. (2011). Quenching the quorum sensing system : potential antibacterial drug targets. Critical Reviews in Microbiology, 37(2), 121–140. https://doi.org/10.3109/1040841X.2010.532479
dcterms.referencesKiratisin, P., Tucker, K. D., & Passador, L. (2002). LasR , a Transcriptional Activator of Pseudomonas aeruginosa Virulence Genes , Functions as a Multimer LasR , a Transcriptional Activator of Pseudomonas aeruginosa Virulence Genes , Functions as a Multimer. Journal of Bacteriology, 184(17), 4912–4919. https://doi.org/10.1128/JB.184.17.4912
dcterms.referencesKoch, W., & Holthausen, M. C. (2001). A Chemist ’ s Guide to Density Functional Theory (2nd ed., Vol. 3).
dcterms.referencesKollef, M. H., Golan, Y., Micek, S. T., Shorr, A. F., & Restrepo, M. I. (2011). Appraising Contemporary Strategies to Combat Multidrug Resistant GramNegative Bacterial Infections – Proceedings and Data From the GramNegative Resistance Summit. Clinical Infectious Diseases 2011, 53, 33–55. https://doi.org/10.1093/cid/cir475
dcterms.referencesKOLLMAN, P., MASSOVA, I., REYES, C., KUHN, B., HUO, S., CHONG, L., … THOMAS, C. (2000). Calculating structures and free energies of complex molecules: Combing molecular mechanics and continuum models. Acc. Chem. Res., 33(12), 889–897.
dcterms.referencesKrom, B. P., Levy, N., Meijler, M. M., & Jabra-rizk, M. A. (2016). R e v i e w Farnesol and Candida albicans : Quorum Sensing or Not Quorum Sensing ? Israel Journal of Chemistry, 56, 295–301. https://doi.org/10.1002/ijch.201500025
dcterms.referencesLade, H., Paul, D., & Kweon, J. H. (2014a). N -Acyl Homoserine LactoneMediated Quorum Sensing with Special Reference to Use of Quorum Quenching Bacteria in Membrane Biofouling Control. BioMed Research International, 2014, 1–25.
dcterms.referencesLade, H., Paul, D., & Kweon, J. H. (2014b). Quorum Quenching Mediated Approaches for Control of Membrane Biofouling. International Journal of Biological Sciences, 10(5), 550–565. https://doi.org/10.7150/ijbs.9028
dcterms.referencesLamb, J. R., Patel, H., Montminy, T., Victoria, E., Iglewski, B. H., & Wagner, V. E. (2003). Functional Domains of the RhlR Transcriptional Regulator of Pseudomonas aeruginosa Functional Domains of the RhlR Transcriptional Regulator of Pseudomonas aeruginosa. Journal of Bacteriology, 185(24), 7129–7139. https://doi.org/10.1128/JB.185.24.7129
dcterms.referencesLandau, L., & Lifshitz, E. (1993). MECHANICS (3rd ed.).
dcterms.referencesLaSarre, B., & Federle, M. J. (2013). Exploiting Quorum Sensing To Confuse Bacterial Pathogens. Microbiology and Molecular Biology Reviews, 77(1), 73–111. https://doi.org/10.1128/MMBR.00046-12
dcterms.referencesLaue, B. E., Jiang, Y., Chhabra, S. R., Jacob, S., Stewart, G. S. A. B., Hardman, A., … Williams, P. (2000). The biocontrol strain Pseudomonas fluorescens F113 produces the Rhizobium small bacteriocin, N-(3-hydroxy7-cis-tetradecenoyl) homoserine lactone, via HdtS, a putative novel Nacylhomoserine lactone synthase. Microbiology, 146(10), 2469–2480. https://doi.org/10.1099/00221287-146-10-2469
dcterms.referencesLavecchia, A., & Di Giovanni, C. (2013). Virtual screening strategies in drug discovery: A critical review. Current Medicinal Chemistry, 20(23), 2839– 2860. https://doi.org/10.2174/09298673113209990001
dcterms.referencesLe-Thi-Thu, H., Casañola-Martín, G. M., Marrero-Ponce, Y., Rescigno, A., Abad, C., & Khan, M. T. H. (2014). A rational workflow for sequential virtual screening of chemical libraries on searching for new tyrosinase inhibitors. Current Topics in Medicinal Chemistry, 14(12), 1473–1485. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0- 84904016156&partnerID=tZOtx3y1
dcterms.referencesLeach, A. R. (2001). Molecular modelling _ principles and applications (Second). Prentice Hall.
dcterms.referencesLeach, A. R., Gillet, V. J., Lewis, R. A., & Taylor, R. (2010). Three-dimensional pharmacophore methods in drug discovery. Journal of Medicinal Chemistry, 53(2), 539–558. https://doi.org/10.1021/jm900817u
dcterms.referencesLeadbetter, J. R., & Greenberg, E. P. (2000). Metabolism of Acyl-Homoserine Lactone Quorum-Sensing Signals by Variovorax paradoxus. JOURNAL OF BACTERIOLOGY, 182(24), 6921–6926.
dcterms.referencesLee, J., & Zhang, L. (2015). The hierarchy quorum sensing network in Pseudomonas aeruginosa, 6(1), 26–41. https://doi.org/10.1007/s13238- 014-0100-x
dcterms.referencesLerat, E., & Moran, N. A. (2004). The Evolutionary History of Quorum-Sensing Systems in Bacteria. Molecular Biology and Evolution, 21(5), 903–913. 95 https://doi.org/10.1093/molbev/msh097
dcterms.referencesLewis, K. (2007). Persister cells , dormancy and infectious disease. Nature Reviews Microbiology, 5(January), 48–56. https://doi.org/10.1038/nrmicro1557
dcterms.referencesLi, Z., & Nair, S. K. (2012). Quorum sensing: How bacteria can coordinate activity and synchronize their response to external signals? Protein Science, 21(10), 1403–1417. https://doi.org/10.1002/pro.2132
dcterms.referencesLindemann, A., Pessi, G., Schaefer, A. L., Mattmann, M. E., Christensen, Q. H., Kessler, A., … Harwood, C. S. (2011). Isovaleryl-homoserine lactone, an unusual branched-chain quorum-sensing signal from the soybean symbiont Bradyrhizobium japonicum. Proceedings of the National Academy of Sciences of the United States of America, 108(40), 16765–70. https://doi.org/10.1073/pnas.1114125108
dcterms.referencesLintz, M. J., Oinuma, K.-I., Wysoczynski, C. L., Greenberg, E. P., & Churchill, M. (2011). Crystal structure of QscR, a Pseudomonas aeruginosa quorum sensing signal receptor. Pnas, 108(38), 15763–15768. https://doi.org/10.1073/pnas.1112398108
dcterms.referencesLionta, E., Spyrou, G., Vassilatis, D. K., & Cournia, Z. (2014). Structure-Based Virtual Screening for Drug Discovery : Principles , Applications and Recent Advances. Current Topics in Medicinal Chemistry, 14, 1923–1938.
dcterms.referencesLipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23, 3–25.
dcterms.referencesLipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2012). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings i. Advanced Drug Delivery Reviews, 64, 4–17. https://doi.org/10.1016/j.addr.2012.09.019
dcterms.referencesLou, Z. Q., Smyth, A. J., Gao, P., Qin, Y., & Farrand, S. K. (2003). Mutational analysis of TraR: Correlating function with molecular structure of a quorumsensing transcriptional activator. Journal of Biological Chemistry, 278(15), 13173–13182. https://doi.org/10.1074/jbc.M210035200
dcterms.referencesLu, Y., Shi, T., Wang, Y., Yang, H., Yan, X., Luo, X., … Zhu, W. (2009). Halogen Bonding s A Novel Interaction for Rational Drug Design ? Journal of Medicinal Chemistry, 52(9), 2854–2862.
dcterms.referencesMaddocks, S. E., & Oyston, P. C. F. (2008). Structure and function of the LysRtype transcriptional regulator ( LTTR ) family proteins. Microbiology, 154, 3609–3623. https://doi.org/10.1099/mic.0.2008/022772-0
dcterms.referencesMaldonado, A. G., Doucet, J. P., Petitjean, M., & Fan, B. T. (2006). Molecular similarity and diversity in chemoinformatics: From theory to applications. Molecular Diversity, 10(1), 39–79. https://doi.org/10.1007/s11030-006- 8697-1
dcterms.referencesMarkou, P., & Apidianakis, Y. (2014). Pathogenesis of intestinal Pseudomonas aeruginosa infection in patients with cancer PROMOTE THE PREVALENCE OF SOURCE OF SYSTEMIC AND REMOTE. Frontiers in Cellular and Infection Microbiology, 3(January), 1–5. https://doi.org/10.3389/fcimb.2013.00115
dcterms.referencesMashburn, L. M., & Whiteley, M. (2005). Membrane vesicles traffic signals and facilitate group activities in a prokaryote. Nature, 437(7057), 422–5. https://doi.org/10.1038/nature03925
dcterms.referencesMattmann, M. E., & Blackwell, H. E. (2010). Small molecules that modulate quorum sensing and control virulence in pseudomonas aeruginosa. Journal of Organic Chemistry, 75(20), 6737–6746. https://doi.org/10.1021/jo101237e
dcterms.referencesMedina-Franco, J. L., Fernández-de Gortaria, E., & Naveja, J. (2015). Química educación. Educación Química, 26, 180–186. https://doi.org/10.1016/j.eq.2015.05.002
dcterms.referencesMiller, B. R., McGee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314– 3321. https://doi.org/10.1021/ct300418h
dcterms.referencesMilton, D. L., Chalker, V. J., Kirke, D., Hardman, A., Cámara, M., & Williams, P. (2001). The LuxM Homologue VanM from Vibrio anguillarum Directs the Synthesis of N and N -Hexanoylhomoserine Lactone The LuxM Homologue VanM from Vibrio anguillarum Directs the Synthesis of N- ( 3- Hydroxyhexanoyl ) homoserine Lactone and N-Hexanoylhomoserine Lact. Journal of Bacteriology, 183(12), 3537–3547. https://doi.org/10.1128/JB.183.12.3537
dcterms.referencesMishra, V., Kashyap, S., & Hasija, Y. (2015). ScienceDirect Ligand based virtual screening for identifying potent inhibitors against viral neuraminidase: An in silico approach. Integrative Medicine Research, 9(1), 20–26. https://doi.org/10.1016/j.jtusci.2014.04.007
dcterms.referencesMOE. (2009). (Molecular Operating Environment). Scientific Computing & Instrumentation. Retrieved from http://www.chemcomp.com/index.htm
dcterms.referencesMontalvo-Acosta, J. J., & Cecchini, M. (2016). Computational Approaches to the Chemical Equilibrium Constant in Protein-ligand Binding. Molecular Informatics, 35(11–12), 555–567. https://doi.org/10.1002/minf.201600052
dcterms.referencesMoore, J. D., Gerdt, J. P., Eibergen, N. R., & Blackwell, H. E. (2014). Active efflux influences the potency of quorum sensing inhibitors in pseudomonas aeruginosa. ChemBioChem, 15(3), 435–442. https://doi.org/10.1002/cbic.201300701
dcterms.referencesMorris, G., & Huey, R. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem, 30(16), 2785– 2791. https://doi.org/10.1002/jcc.21256.AutoDock4
dcterms.referencesNealson, K. H., Platt, T., & Hastings, J. W. (1970). Cellular control of the synthesis and activity of the bacterial luminescent system. Journal of Bacteriology, 104(1), 313–322.
dcterms.referencesO’Brien, K. T., Noto, J. G., Nichols-O’Neill, L., & Perez, L. J. (2015). Potent irreversible inhibitors of LasR quorum sensing in Pseudomonas aeruginosa. ACS Medicinal Chemistry Letters, 6(2), 162–167. https://doi.org/10.1021/ml500459f
dcterms.referencesO’Connell, K. M. G., Hodgkinson, J. T., Sore, H. F., Welch, M., Salmond, G. P. C., & Spring, D. R. (2013). Combating multidrug-resistant bacteria: Current strategies for the discovery of novel antibacterials. Angewandte Chemie - International Edition, 52(41), 10706–10733. https://doi.org/10.1002/anie.201209979
dcterms.referencesO’Reilly, M. C., & Blackwell, H. E. (2016). Structure-Based Design and Biological Evaluation of Triphenyl Scaffold-Based Hybrid Compounds as Hydrolytically Stable Modulators of a LuxR-Type Quorum Sensing Receptor. ACS Infectious Diseases, 2(1), 32–38. https://doi.org/10.1021/acsinfecdis.5b00112
dcterms.referencesPalmer, A. G., Streng, E., & Blackwell, H. E. (2011). Attenuation of virulence in pathogenic bacteria using synthetic quorum-sensing modulators under native conditions on plant hosts. ACS Chemical Biology, 6(12), 1348–56. https://doi.org/10.1021/cb200298g
dcterms.referencesParr, R. G., & Yang, W. (1989). Density-Functional Theory of Atoms andMolecules. (O. U. Press, Ed.). New York.
dcterms.referencesParsek, M. R., Val, D. L., Hanzelka, B. L., Cronan, J. E., & Greenberg, E. P. (1999). Acyl homoserine-lactone quorum-sensing signal generation. Proceedings of the National Academy of Sciences of the United States of America, 96(8), 4360–5. https://doi.org/10.1073/pnas.96.8.4360
dcterms.referencesQing, X., Xiao, Y. L., De Raeymaeker, J., Tame, RH, J., Zhang, K., De Maeyer, M., & Arnout, V. (2014). Pharmacophore modeling : advances , limitations , and current utility in drug discovery. Journal of Receptor, Ligand and Channel Research, 7, 81–92.
dcterms.referencesRampioni, G., Leoni, L., & Williams, P. (2014). Bioorganic Chemistry The art of antibacterial warfare : Deception through interference with quorum sensing – mediated communication. BIOORGANIC CHEMISTRY, 55, 60–68. https://doi.org/10.1016/j.bioorg.2014.04.005
dcterms.referencesRarey, M., Kramer, B., Lengauer, T., & Klebe, G. (1996). A Fast Flexible Docking Method using an Incremental Construction Algorithm. Journal of Molecular Biology, 261(3), 470–489.
dcterms.referencesRasmussen, T. B., & Givskov, M. (2006). Quorum-sensing inhibitors as antipathogenic drugs. International Journal of Medical Microbiology, 296, 149– 161. https://doi.org/10.1016/j.ijmm.2006.02.005
dcterms.referencesRipphausen, P., Nisius, B., & Bajorath, J. (2011). State-of-the-art in ligandbased virtual screening. FEATURES Drug Discovery Today, 16(May), 372– 376. https://doi.org/10.1016/j.drudis.2011.02.011
dcterms.referencesRojas-Badía, M. M. (2011). Quorum sensing in beneficial plant-bacteria associations. Revista Colombiana de Biotecnologia, 13(2), 135–143.
dcterms.referencesRumbaugh, K. P. (2011). Quorum Sensing Methods and Protocols. Methods in molecular biology (Clifton, N.J.) ; v. 692. 1064-3745. https://doi.org/10.1007/s13398-014-0173-7.2
dcterms.referencesRutherford, S., & Bassler, B. (2012). Bacterial Quorum Sensing : Its Role in Virulence and Possibilities for Its Control. Cold Spring Harbor Laboratory Press, 1–26.
dcterms.referencesRutherford, 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(11), 1–25. https://doi.org/10.1101/cshperspect.a012427
dcterms.referencesRyckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. https://doi.org/10.1016/0021-9991(77)90098-5
dcterms.referencesSadikot, R. T., Blackwell, T. S., Christman, J. W., & Prince, A. S. (2005). Pathogen – Host Interactions in Pseudomonas aeruginosa Pneumonia RESPIRATORY INFECTIONS. American Journal of Respiratory and Critical Care Medicine, 171(11), 1209–1223. https://doi.org/10.1164/rccm.200408-1044SO
dcterms.referencesSaldívar-gonzález, F., & Medina-franco, F. D. P. J. L. (2017). Descubrimiento y desarrollo de fármacos: un enfoque computacional. Educación Química, 28(1), 51–58. https://doi.org/10.1016/j.eq.2016.06.002
dcterms.referencesSchaefer, A. L., Greenberg, E. P., Oliver, C. M., Oda, Y., Huang, J. J., BittanBanin, G., … Harwood, C. S. (2008). A new class of homoserine lactone quorum-sensing signals. Nature, 454(7204), 595–599. https://doi.org/10.1038/nature07088
dcterms.referencesSchneider, G., & Fechner, U. (2005). Computer-based de novo design of druglike molecules. Nature Reviews Drug Discovery, 4(8), 649–663. https://doi.org/10.1038/nrd1799
dcterms.referencesSchuster, M., Sexton, D. J., Diggle, S. P., & Greenberg, E. P. (2013). Acylhomoserine lactone quorum sensing: from evolution to application. Annual Review of Microbiology, 67(May 2013), 43–63. https://doi.org/10.1146/annurev-micro-092412-155635
dcterms.referencesScreening, H., Borlee, B. R., Geske, G. D., Blackwell, H. E., & Handelsman, J. (2010). Identification of Synthetic Inducers and Inhibitors of the QuorumSensing Regulator LasR in Pseudomonas aeruginosa by. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 76(24), 8255–8258. https://doi.org/10.1128/AEM.00499-10
dcterms.referencesSen, S., Farooqui, N. A., Easwari, T. S., & Roy, B. (2012). CoMFA -3D QSAR APPROCH IN DRUG DESIGN. International Journal of Research and Development in Pharmacy and Life Sciences, 1(4), 167–175.
dcterms.referencesSheridan, R. P., & Kearsley, S. K. (2002). Why do we need so many chemical simialrity search methods? Ddt, 7(17), 903–911.
dcterms.referencesSherrill, D. (2000). An Introduction to Hartree-Fock Molecular Orbital Theory What. Georgia Inst. of Technology, 1–8.
dcterms.referencesSippl, W. (2000). Receptor-based 3D QSAR analysis of estrogen receptor ligands – merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods ∗. Journal of ComputerAided Molecular Design, 14, 559–572.
dcterms.referencesSmith, R. S., & Iglewski, B. H. (2003). Pseudomonas aeruginosa quorum sensing as a potential antimicrobial target. Journal of Clinical Investigation, 112(10), 1460–1465. https://doi.org/10.1172/JCI200320364
dcterms.referencesSoulère, L., Frezza, M., Queneau, Y., & Doutheau, A. (2007). Exploring the active site of acyl homoserine lactones-dependent transcriptional regulators with bacterial quorum sensing modulators using molecular mechanics and docking studies. Journal of Molecular Graphics and Modelling, 26(2), 581– 590. https://doi.org/10.1016/j.jmgm.2007.04.004
dcterms.referencesSoulère, L., Sabbah, M., Fontaine, F., Queneau, Y., & Doutheau, A. (2010). LuxR-dependent quorum sensing: Computer aided discovery of new inhibitors structurally unrelated to N-acylhomoserine lactones. Bioorganic and Medicinal Chemistry Letters, 20(15), 4355–4358. https://doi.org/10.1016/j.bmcl.2010.06.081
dcterms.referencesStevens, A. M., Dolan, K. M., & Greenberg, E. P. (1994). Synergistic binding of the Vibrio fischeri LuxR transcriptional activator domain and RNA polymerase to the lux promoter region. Proceedings of the National Academy of Sciences of the United States of America, 91(26), 12619– 12623. https://doi.org/10.1073/pnas.92.8.3631a
dcterms.referencesStewart, J. J. P. (1989). Optimization of Parameters for Semiempirical Methods .2. Applications. J. Comput. Chem., 10(2), 221–264. https://doi.org/10.1002/jcc.540100209
dcterms.referencesStewart, J. J. P. (2013). Optimization of parameters for semiempirical methods VI : more modifications to the NDDO approximations and re-optimization of parameters. J Mol Model, 19, 1–32. https://doi.org/10.1007/s00894-012- 1667-x
dcterms.referencesStumpfe, D., & Bajorath, J. (2011). Similarity searching. Computational Molecular Science, 1(April), 260–282. https://doi.org/10.1002/wcms.23
dcterms.referencesStumpfe, D., & Bajorath, J. (2012). Exploring activity cliffs in medicinal chemistry. Journal of Medicinal Chemistry, 55(7), 2932–2942. https://doi.org/10.1021/jm201706b
dcterms.referencesStumpfe, D., León, A. de, Dimova, D., & Bajorath, J. (2014). Follow up: Advancing the activity cliff concept, part II ANRT biblio Chemistry ML NeuralNets QSAR. F1000Research, 199, 1–11. https://doi.org/10.12688/f1000research.3788.1
dcterms.referencesSuneby, E. G., Herndon, L. R., & Schneider, T. L. (2017). Pseudomonas aeruginosa LasR·DNA Binding Is Directly Inhibited by Quorum Sensing Antagonists. ACS Infectious Diseases, acsinfecdis.6b00163. https://doi.org/10.1021/acsinfecdis.6b00163
dcterms.referencesThiel, V., Kunze, B., Verma, P., Wagner-Döbler, I., & Schulz, S. (2009). New structural variants of homoserine lactones in bacteria. ChemBioChem, 10(11), 1861–1868. https://doi.org/10.1002/cbic.200900126
dcterms.referencesTian, S., Wang, J., Li, Y., Xu, X., & Hou, T. (2012). Drug-likeness analysis of traditional chinese medicines: Prediction of drug-likeness using machine learning approaches. Molecular Pharmaceutics, 9(10), 2875–2886. https://doi.org/10.1021/mp300198d
dcterms.referencesTodeschini, R., & Consonni, V. (2009). Chemometrics in QSAR. Comprehensive Chemometrics, 4, 129–172
dcterms.referencesTomasz, A. (1965). Control of the competent state in Pneumococcus by a hormone-like cell product. Nature, 208(5006), 155–159. https://doi.org/10.1038/208155a0
dcterms.referencesTurner, K. H., Everett, J., Trivedi, U., Rumbaugh, K. P., & Whiteley, M. (2014). Requirements for Pseudomonas aeruginosa Acute Burn and Chronic Surgical Wound Infection. PLOS Genetics, 10(7), 1–12. https://doi.org/10.1371/journal.pgen.1004518
dcterms.referencesTurner, K. H., Wessel, A. K., Palmer, G. C., Murray, J. L., & Whiteley, M. (2015). Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum. Proceedings of the National Academy of Sciences of the United States of America, 112(13), 4110–5. https://doi.org/10.1073/pnas.1419677112
dcterms.referencesVannini, A., Volpari, C., Gargioli, C., Muraglia, E., Cortese, R., De Francesco, R., … Di Marco, S. (2002). The crystal structure of the quorum sensing protein TraR bound to its autoinducer and target DNA. EMBO Journal, 21(17), 4393–4401. https://doi.org/10.1093/emboj/cdf459
dcterms.referencesVistoli, G., Pedretti, A., & Testa, B. (2008). Assessing drug-likeness - what are we missing? Drug Discovery Today, 13(7–8), 285–294. https://doi.org/10.1016/j.drudis.2007.11.007
dcterms.referencesVyas, V., Jain, A., Jain, A., & Gupta, A. (2008). Virtual screening: A fast tool for drug design. Scientia Pharmaceutica, 76(3), 333–360. https://doi.org/10.3797/scipharm.0803-03
dcterms.referencesWalters, W. P., & Murcko, M. A. (2002). Prediction of “drug-likeness.” Advanced Drug Delivery Reviews, 54(3), 255–271. https://doi.org/10.1016/S0169- 409X(02)00003-0
dcterms.referencesWang, J. M., Wolf, R. M., Caldwell, J. W., Kollman, P. a, & Case, D. a. (2004). Development and testing of a general amber force field. J. Comput. Chem., 25(9), 1157–1174. https://doi.org/10.1002/jcc.20035
dcterms.referencesWarren, G. L., Andrews, C. V, Capelli, a, Clarke, B., LaLonde, J., Lambert, M. H., … Head, M. S. (2006). A critical assessment of docking programs and scoring functions.Capelli, A.LaLonde, J.Semus, S. F.Head, M. S. J. Med. Chem., (49), 5912–5931.
dcterms.referencesWaters, C. M., & Bassler, B. L. (2005). Quorum Sensing : Cell-to-Cell Communication in Bacteria. Annual Reviews in Cell Development Biology, 21(1), 319–346. https://doi.org/10.1146/annurev.cellbio.21.012704.131001
dcterms.referencesWatson, W. T., Minogue, T. D., Val, D. L., von Bodman, S. B., & Churchill, M. E. a. (2002). Structural basis and specificity of acyl-homoserine lactone signal production in bacterial quorum sensing. Molecular Cell, 9(3), 685–694. https://doi.org/10.1016/S1097-2765(02)00480-X
dcterms.referencesWelsh, M. A., & Blackwell, H. E. (2016a). Chemical Genetics Reveals Environment-Specific Roles for Quorum Sensing Circuits in Pseudomonas aeruginosa. Cell Chemical Biology, 23(3), 361–369. https://doi.org/10.1016/j.chembiol.2016.01.006
dcterms.referencesWelsh, M. A., & Blackwell, H. E. (2016b). Chemical probes of quorum sensing: from compound development to biological discovery. FEMS Microbiology Reviews, 40(5), 774–794. https://doi.org/10.1093/femsre/fuw009
dcterms.referencesWermuth, C. G., Ganellin, C. R., Lindberg, P., & Mitscher, L. A. (1998). GLOSSARY OF TERMS USED IN MEDICINAL CHEMISTRY. Pure Appl. Chem, 70(5), 1129–1143.
dcterms.referencesWilliams, P., Winzer, K., Chan, W. C., & Cámara, M. (2007). Look who’s talking: communication and quorum sensing in the bacterial world. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 362(1483), 1119–1134. https://doi.org/10.1098/rstb.2007.2039
dcterms.referencesWinzer, K., Hardie, K. R., & Williams, P. (2002). Bacterial cell-to-cell communication : sorry , can ’ t talk now — gone to lunch ! Bacterial Cell-toCell Communication, 5, 216–222.
dcterms.referencesXu, X., & Goddard, W. A. (2004). The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties. Proceedings of the National Academy of Sciences of the United States of America, 101(9), 2673–2677. https://doi.org/10.1073/pnas.0308730100
dcterms.referencesYao, Y., Martinez-Yamout, M. A., Dickerson, T. J., Brogan, A. P., Wright, P. E., & Dyson, H. J. (2006). Structure of the Escherichia coli quorum sensing protein SdiA: Activation of the folding switch by acyl homoserine lactones. Journal of Molecular Biology, 355(2), 262–273. https://doi.org/10.1016/j.jmb.2005.10.041
dcterms.referencesYates, E. A., Philipp, B., Buckley, C., Atkinson, S., Chhabra, S. R., Sockett, R. E., … Dessaux, Y. (2002). N -Acylhomoserine Lactones Undergo Lactonolysis in a pH- , Temperature- , and Acyl Chain Length-Dependent Manner during Growth of Yersinia pseudotuberculosis and Pseudomonas aeruginosa. INFECTION AND IMMUNITY, 70(10), 5635–5646. https://doi.org/10.1128/IAI.70.10.5635
dcterms.referencesYoung, D. C. (2001). COMPUTATIONAL CHEMISTRY A Practical Guide for Applying Techniques to Real-World Problems. New York (Vol. 9). https://doi.org/10.1002/jat.1666
dcterms.referencesZheng, Y., & Sintim, H. O. (2014). Molecular insights into how ligands activate or inactivate LasR. Chemistry and Biology, 21(10), 1261–1263. https://doi.org/10.1016/j.chembiol.2014.10.001
dcterms.referencesZhu, T., Cao, S., Su, P.-C., Patel, R., Shah, D., Chokshi, H. B., … Johnson, M. E. (2013). Practical, Hit Identification and Optimization in Virtual Screening: Analysis, Recommendations Based Upon a Critical Literature. Journal of Medicinal Chemistry, 56(17), 6560–6572. https://doi.org/10.1021/jm301916b.Hit
dcterms.referencesZou, Y., & Nair, S. K. (2009a). Molecular Basis for the Recognition of Structurally Distinct Autoinducer Mimics by the Pseudomonas aeruginosa LasR Quorum-Sensing Signaling Receptor. Chemistry and Biology, 16(9), 961–970. https://doi.org/10.1016/j.chembiol.2009.09.001
dcterms.referencesZou, Y., & Nair, S. K. (2009b). Molecular Basis for the Recognition of Structurally Distinct Autoinducer Mimics by the Pseudomonas aeruginosa LasR Quorum-Sensing Signaling Receptor. Chemistry and Biology, 16(9), 961–970. https://doi.org/10.1016/j.chembiol.2009.09.001
dcterms.referencesAbagyan, R., Totrov, M., & Kuznetsov, D. (1994). New Method for Protein Modeling and Design : Applications to Docking and Structure Prediction from the Distorted Native Conformation. Journal of Computational Chemistry, 15(5), 488–506.
dcterms.referencesAdcock, S. A., & McCammon, J. A. (2006). Molecular dynamics: Survey of methods for simulating the activity of proteins. Chemical Reviews, 106(5), 1589–1615. https://doi.org/10.1021/cr040426m
dcterms.referencesAhlgren, N. a, Harwood, C. S., Schaefer, A. L., Giraud, E., & Greenberg, E. P. (2011). Aryl-homoserine lactone quorum sensing in stem-nodulating photosynthetic bradyrhizobia. Proceedings of the National Academy of Sciences of the United States of America, 108(17), 7183–7188. https://doi.org/10.1073/pnas.1103821108
dcterms.referencesAhumedo, M., Díaz, A., & Vivas-Reyes, R. (2010). Theoretical and structural analysis of the active site of the transcriptional regulators LasR and TraR, using molecular docking methodology for identifying potential analogues of acyl homoserine lactones (AHLs) with anti-quorum sensing activity. European Journal of Medicinal Chemistry, 45(2), 608–615. https://doi.org/10.1016/j.ejmech.2009.11.004
dcterms.referencesAhumedo, M., Drosos, J. C., & Vivas-Reyes, R. (2014a). Application of molecular docking and ONIOM methods for the description of interactions between anti-quorum sensing active (AHL) analogues and the Pseudomonas aeruginosa LasR binding site. Molecular bioSystems, 10(5), 1162–71. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/24626770
dcterms.referencesAhumedo, M., Drosos, J. C., & Vivas-Reyes, R. (2014b). Application of molecular docking and ONIOM methods for the description of interactions between anti-quorum sensing active (AHL) analogues and the Pseudomonas aeruginosa LasR binding site. Molecular bioSystems, 10(5), 1162–71. https://doi.org/10.1039/c3mb70181f
dcterms.referencesAlberto, G., & Rossello, M. (2013). Quorum sensing en bacterias y levaduras. Medicina Clinica, 141(8), 353–357.
dcterms.referencesAmara, N., Mashiach, R., Amar, D., Krief, P., Spieser, A. H., Bottomley, M. J., … Meijler, M. M. (2009). Covalent Inhibition of Bacterial Quorum Sensing, (8), 197–201. https://doi.org/10.1002/cbic.201500676
dcterms.referencesAtkinson, S., & Williams, P. (2009). Quorum sensing and social networking in the microbial world. Journal of the Royal Society, Interface / the Royal Society, 6(40), 959–78. https://doi.org/10.1098/rsif.2009.0203
dcterms.referencesAuffinger, P., Hays, F. A., Westhof, E., & Ho, P. S. (2004). Halogen bonds in biological molecules. Proc. Natl. Acad. Sci., 101(48), 16789–16794.
dcterms.referencesBai, A. J., & Rai, V. R. (2011). Bacterial Quorum Sensing and Food Industry. Comprehensive Reviews in Food Science and Food Safety, 10(3), 183– 193. https://doi.org/10.1111/j.1541-4337.2011.00150.x
dcterms.referencesBassler, B. L., & Losick, R. (2006). Bacterially Speaking. Cell, 125(2), 237–246. https://doi.org/10.1016/j.cell.2006.04.001
dcterms.referencesBassler, B. L., & Ng, W. (2009). NIH Public Access. Annu. Rev. Genet, 43, 197– 222. https://doi.org/10.1146/annurev-genet-102108-134304.Bacterial
dcterms.referencesBayly, C. C. I., Cieplak, P., Cornell, W. D., & Kollman, P. a. (1993). A wellbehaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. The Journal of Physical …, 97, 10269–10280. https://doi.org/10.1021/j100142a004
dcterms.referencesBhargava, N., Sharma, P., & Capalash, N. (2010). Quorum sensing in Acinetobacter : an emerging pathogen, 36(July), 349–360. https://doi.org/10.3109/1040841X.2010.512269
dcterms.referencesBlackwell, H. E., & Fuqua, C. (2011). Introduction to bacterial signals and chemical communication. Chemical Reviews, 111(1), 1–3. https://doi.org/10.1021/cr100407j
dcterms.referencesBlankenship, J. R., & Mitchell, A. P. (2006). How to build a biofilm: a fungal perspective. Current Opinion in Microbiology, 9(6), 588–594. https://doi.org/10.1016/j.mib.2006.10.003
dcterms.referencesBonomo, R. A., & Szabo, D. (2006). Mechanisms of Multidrug Resistance in Acinetobacter Species and Pseudomonas aeruginosa. Clinical Infectious Diseases, 44106, 49–56.
dcterms.referencesBottomley, M. J., Muraglia, E., Bazzo, R., & Carfì, A. (2007). Molecular insights into quorum sensing in the human pathogen Pseudomonas aeruginosa from the structure of the virulence regulator LasR bound to its autoinducer. Journal of Biological Chemistry, 282(18), 13592–13600. https://doi.org/10.1074/jbc.M700556200
dcterms.referencesBoucher, H. W., Talbot, G. H., Benjamin, D. K., Bradley, J., Guidos, R. J., Jones, R. N., … Gilbert, D. (2013). 10 x ’20 Progress--development of new drugs active against gram-negative bacilli: an update from the Infectious Diseases Society of America. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America, 56(12), 1685–94. https://doi.org/10.1093/cid/cit152
dcterms.referencesBrown, S. A., Palmer, K. L., & Whiteley, M. (2008). Revisiting the host as a growth medium. MICROBIOLOGY, 6, 657–666. https://doi.org/10.1038/nrmicro1955
dcterms.referencesBurton, E. O., Read, H. W., Pellitteri, M. C., & Hickey, W. J. (2005). Identification of acyl-homoserine lactone signal molecules produced by Nitrosomonas europaea strain Schmidt. Applied and Environmental Microbiology, 71(8), 4906–4909. https://doi.org/10.1128/AEM.71.8.4906- 4909.2005
dcterms.referencesCai, W., Li, J., & Yip, S. (2012). Molecular Dynamics. Comprehensive Nuclear Materials, 1, 249–265. https://doi.org/10.1016/B978-0-08-056033-5.00128- 2
dcterms.referencesCamilli, A., & Bassler, B. . (2006). NIH Public Access. Nature Reviews. Microbiology, 311(5764), 1113–1116. https://doi.org/10.1126/science.1121357.Bacterial
dcterms.referencesCapilato, J. N., Philippi, S., Reardon, T., McConnell, A., Oliver, D., Warren, A., … Perez, L. J. (2016). Development of a novel series of non-natural triaryl agonists and antagoinsts of the Pseudomonas aeruginosa LasR quorum sensing receptor. Bioorganic & Medicinal Chemistry. https://doi.org/10.1016/j.bmc.2016.10.021
dcterms.referencesCase, D., Babin, V., Berryman, J. T., Betz, R. M., Cai, Q., Cerutti, D. S., … Kollman, P. A. (2014). Amber 14. San Francisco. Retrieved from http://ambermd.org/contributors%0D
dcterms.referencesCavasotto, C. (2016). In Silico drug Discovery and Design Theory, Methods, Challenges, and Applications.
dcterms.referencesCegelski, L., Marshall, G. R., Eldridge, G. R., & Hultgren, S. J. (2008). NIH Public Access. Nat Rev Microbiol, 6(1), 17–27.
dcterms.referencesCereto-Massagué, A., Ojeda, M. J., Valls, C., Mulero, M., Garcia-Vallvé, S., & Pujadas, G. (2015). Molecular fingerprint similarity search in virtual screening. Methods, 71(C), 58–63. https://doi.org/10.1016/j.ymeth.2014.08.005
dcterms.referencesChakrabarti, S., & Sowdhamini, R. (2003). Functional sites and evolutionary connections of acylhomoserine lactone synthases. Protein Engineering, 16(4), 271–278. https://doi.org/DOI 10.1093/proeng/gzg031
dcterms.referencesChen, G., Swem, L. R., Swem, D. L., Stauff, D. L., O'Loughlin, C. T., Jeffrey, P. D., … Hughson, F. M. (2011). A Strategy for Antagonizing Quorum Sensing. Molecular Cell, 42(2), 199–209. https://doi.org/10.1016/j.molcel.2011.04.003
dcterms.referencesCheng, T., Li, Q., Zhou, Z., Wang, Y., & Bryant, S. H. (2012). Structure-based virtual screening for drug discovery: a problem-centric review. The AAPS Journal, 14(1), 133–41. https://doi.org/10.1208/s12248-012-9322-0
dcterms.referencesChipot, C. (2014). Frontiers in free-energy calculations of biological systems. Computational Molecular Science, 4(1), 71–89. https://doi.org/10.1002/wcms.1157
dcterms.referencesCho, T., Nagao, J., Imayoshi, R., Kaminishi, H., Aoyama, T., & Nakayama, H. (2010). Quorum Sensing and Morphological Regulation in the Pathogenic Fungus Candida albicans. Journal of Oral Biosciences, 52(3), 233–239. https://doi.org/10.1016/S1349-0079(10)80026-X
dcterms.referencesChristensen, Q. H., Brecht, R. M., Dudekula, D., Greenberg, E. P., & Nagarajan, R. (2014). Evolution of Acyl-Substrate Recognition by a Family of AcylHomoserine Lactone Synthases. PLoS ONE, 9(11), 1–8. https://doi.org/10.1371/journal.pone.0112464
dcterms.referencesChurchill, M. E. A., & Chen, L. (2011). NIH Public Access (Vol. 111). https://doi.org/10.1021/cr1000817.Structural
dcterms.referencesCramer, C. J. (2004). Essentials of Computational Chemistry Theories and Models. New York (Second Edi). https://doi.org/10.1037/023990
dcterms.referencesCramer, R. D., Patterson, D. E., & Bunce, J. D. (1988). Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc, 110(12), 5959–5967.
dcterms.referencesCrousilles, A., Maunders, E., Bartlett, S., Fan, C., Abdelhamid, Y., Baker, Y., … Welch, M. (2015). Which microbial factors really are important in Pseudomonas aeruginosa infections ? Future Microbiology, 10(11), 1825– 1836.
dcterms.referencesCuevas, G., & Cortés, F. (2003). Introducción a la Química Computacional.
dcterms.referencesDanishuddin, M., & Khan, A. U. (2015). Structure based virtual screening to discover putative drug candidates: Necessary considerations and successful case studies. Methods, 71(C), 135–145. https://doi.org/10.1016/j.ymeth.2014.10.019
dcterms.referencesde Souza, O. N., & Ornstein, R. L. (1997). Effect of periodic box size on aqueous molecular dynamics simulation of a DNA dodecamer with particlemesh Ewald method. Biophysical Journal, 72(6), 2395–7. https://doi.org/10.1016/S0006-3495(97)78884-2
dcterms.referencesDekimpe, V., & Déziel, E. (2009). Revisiting the quorum-sensing hierarchy in Pseudomonas aeruginosa : the transcriptional regulator RhlR regulates LasR-specific factors. Microbiology, 155, 712–723. https://doi.org/10.1099/mic.0.022764-0
dcterms.referencesDennington, R., Keith, T., & Millam, J. (2009). GaussView. Semichem Inc., Shawnee Mission KS.
dcterms.referencesDing, X., Yin, B., Qian, L., Zeng, Z., Yang, Z., Li, H., … Zhou, S. (2011). Screening for novel quorum-sensing inhibitors to interfere with the formation of Pseudomonas aeruginosa biofilm. Journal of Medical Microbiology, 60, 1827–1834. https://doi.org/10.1099/jmm.0.024166-0
dcterms.referencesDong, Y., Xu, J., Li, X., & Zhang, L. (2000). AiiA , an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of Erwinia carotovora. Proc. Natl. Acad. Sci, 97(7), 3526–3531.
dcterms.referencesDonlan, R. M., & Costerton, J. W. (2002). Biofilms : Survival Mechanisms of Clinically Relevant Microorganisms. CLINICAL MICROBIOLOGY REVIEWS, 15(2), 167–193. https://doi.org/10.1128/CMR.15.2.167
dcterms.referencesDoshi, H. K., Chua, K., Kagda, F., & Tambyah, P. A. (2011). Multi drug resistant pseudomonas infection in open fractures post definitive fixation leading to limb loss : A report of three cases. International Journal of Case Reports and Images, 2(5), 1–6. https://doi.org/10.5348/ijcri-2011-05-31-CS-1
dcterms.referencesDuan, Y., Wu, C., Chowdhury, S. S., Lee, M. C., Xiong, G., Zhang, W., … Kollman, P. (2003). A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry, 24(16), 1999–2012. https://doi.org/10.1002/jcc.10349
dcterms.referencesEberhard, C., Dew, W., Science, D. R., Eberhard, A., Burlingame, A. L., Kenyon, G. L., … Oppenheimer, N. J. (1981). Structural Identification of Autoinducer of Photobacterium fischeri. Biochemistry 1981, 20, 2444– 2449.
dcterms.referencesFolkesson, A., Jelsbak, L., Yang, L., Johansen, H. K., Ciofu, O., Høiby, N., & Molin, S. (2012). Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway : an evolutionary perspective. Nature Reviews Microbiology, 10(12), 841–851. https://doi.org/10.1038/nrmicro2907
dcterms.referencesFrei, R., Breitbach, A. S., & Blackwell, H. E. (2012). 2-Aminobenzimidazole Derivatives Strongly Inhibit and Disperse Pseudomonas aeruginosa Biofilms ** Angewandte. Angew. Chem. Int, (51), 1–5. https://doi.org/10.1002/anie.201109258
dcterms.referencesFriesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., … Shenkin, P. S. (2004). Glide : A New Approach for Rapid , Accurate Docking and Scoring . 1 . Method and Assessment of Docking Accuracy. J. Med. Chem, 47(7), 1739–1749.
dcterms.referencesFrisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A. et al. (2009). Gaussian 09. Wallingford: Gaussian, Inc.
dcterms.referencesFrisch, J. B., & Foresman, A. (1994). Exploring_Chemistry_With_Electronic_Structure_Methods.
dcterms.referencesFuqua, C., & Greenberg, E. P. (2002). Listening in on bacteria: acyl-homoserine lactone signalling. Nature Reviews in Molecular Cell Biology, 3(September), 685–695. https://doi.org/10.1038/nrm907
dcterms.referencesFuqua, W. C., Winans, S. C., & Greenberg, E. P. (1994). Quorum sensing in bacteria: The LuxR-LuxI family of cell density- responsive transcriptional regulators. Journal of Bacteriology, 176(2), 269–275. https://doi.org/10.1111/j.1462-5822.2006.00734.x
dcterms.referencesGalloway, W. R. J. D., Hodgkinson, J. T., Bowden, S. D., Welch, M., & Spring, D. R. (2011). Quorum sensing in Gram-negative bacteria: Small-molecule modulation of AHL and AI-2 quorum sensing pathways. Chemical Reviews, 111(1), 28–67. https://doi.org/10.1021/cr100109t
dcterms.referencesGalloway, W. R. J. D., 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, 20(9), 449–458. https://doi.org/10.1016/j.tim.2012.06.003
dcterms.referencesGenheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 441(October), 1–13. https://doi.org/10.1517/17460441.2015.1032936
dcterms.referencesGenheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 441(October), 1–13. https://doi.org/10.1517/17460441.2015.1032936
dcterms.referencesGerdt, J. P., McInnis, C. E., Schell, T. L., Rossi, F. M., & Blackwell, H. E. (2014a). Mutational analysis of the quorum-sensing receptor LasR reveals interactions that govern activation and inhibition by nonlactone ligands. Chemistry and Biology, 21(10), 1361–1369. https://doi.org/10.1016/j.chembiol.2014.08.008
dcterms.referencesGeske, G. D., Mattmann, M. E., & Blackwell, H. E. (2008). Evaluation of a focused library of N-aryl l-homoserine lactones reveals a new set of potent quorum sensing modulators. Bioorganic and Medicinal Chemistry Letters, 18(22), 5978–5981. https://doi.org/10.1016/j.bmcl.2008.07.089
dcterms.referencesGeske, G. D., Neill, J. C. O., & Blackwell, H. E. (2008). NIH Public Access, 37(7), 1432–1447. https://doi.org/10.1039/b703021p.Expanding
dcterms.referencesGeske, G. D., O’Neill, J. C., Miller, D. M., Mattmann, M. E., & Blackwell, H. E. (2007). Modulation of Bacterial Quorum Sensing with Synthetic Ligands: Systematic Evaluation of N -Acylated Homoserine Lactones in Multiple Species and New Insights into Their Mechanisms of Action. Journal of the American Chemical Society, 129(44), 13613–13625. https://doi.org/10.1021/ja074135h
dcterms.referencesGodbout, N., Salahub, D. R., Andzelm, J., & Wimmer, E. (1992). Optimization of Gaussian-type basis sets for local spin density functional calculations. Part I. Boron through neon, optimization technique and validation. Canadian Journal of Chemistry, 70(2), 560–571. https://doi.org/10.1139/v92-079
dcterms.referencesGonzález, J. E., & Marketon, M. M. (2003). Quorum sensing in nitrogen-fixing rhizobia. Microbiology and Molecular Biology Reviews : MMBR, 67(4), 574– 92. https://doi.org/10.1128/MMBR.67.4.574
dcterms.referencesGoodisman, J. (1973). Diatomic interaction potential theory. Academic Press, 1.
dcterms.referencesGould, T., Schweizer, H., & Churchill, M. (2004). Structure of the Pseudomonas aeruginosa acyl- homoserinelactone synthase LasI. Molecular Microbiology (2004), 53(4), 1135–1146. https://doi.org/10.1111/j.1365- 2958.2004.04211.x
dcterms.referencesGutiérres-de-Terán, H. (2004). Modelización molecular de los receptores de adenosina y sus ligandos en el marco de diseño de fármacos asistido por ordenador, 28–29. Retrieved from http://hdl.handle.net/10230/11902
dcterms.referencesHanzelka, B. L., & Greenberg, E. P. (1996). Quorum sensing in Vibrio fischeri : evidence that S-adenosylmethionine is the amino acid substrate for autoinducer synthesis . Quorum Sensing in Vibrio fischeri : Evidence that S -Adenosylmethionine Is the Amino Acid Substrate for Autoinducer Synthesis. Journal of Bacteriology, 178(17), 5291–5294.
dcterms.referencesHartmann, A., & Schikora, A. (2012). Quorum Sensing of Bacteria and TransKingdom Interactions of N -Acyl Homoserine Lactones with Eukaryotes. J Chem Ecol, 38(6), 704–713. https://doi.org/10.1007/s10886-012-0141-7
dcterms.referencesHenke, J. M., & Bassler, B. L. (2004). Bacterial social engagements. Trends in Cell Biology, 14(11), 648–656. https://doi.org/10.1016/j.tcb.2004.09.012
dcterms.referencesHense, B. A., & Schuster, M. (2015). Core principles of bacterial autoinducer systems. Microbiology and Molecular Biology Reviews : MMBR, 79(1), 153–69. https://doi.org/10.1128/MMBR.00024-14
dcterms.referencesHentzer, M., & Givskov, M. (2003). Pharmacological inhibition of quorum sensing for the treatment of chronic bacterial infections. J. Clin. Invest., 112(9), 1300–1307. https://doi.org/10.1172/JCI200320074.One
dcterms.referencesHentzer, M., Riedel, K., Rasmussen, T. B., Heydorn, A., Andersen, J. B., Parsek, M. R., … Givskov, M. (2002). Inhibition of quorum sensing in Pseudomonas aeruginosa biofilm bacteria by a halogenated furanone compound. Microbiology, 148, 87–102.
dcterms.referencesHETÉNYI, C., & VAN DER SPOEL, D. (2002). Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Science (2002), 11, 1729–1737. https://doi.org/10.1110/ps.0202302.the
dcterms.referencesHomeyer, N., & Gohlke, H. (2012). Free Energy Calculations by the Molecular Mechanics Poisson-Boltzmann Surface Area Method. Molecular Informatics, 31, 114–122. https://doi.org/10.1002/minf.201100135
dcterms.referencesHomeyer, N., & Gohlke, H. (2013). Advances in molecular dynamics simulations and free-energy calculations relevant for drug design. In M. A. Lill (Ed.), In Silico Drug Discovery and Design (pp. 51–64).
dcterms.referencesHuang, J. J., Han, J., Zhang, L., & Leadbetter, J. R. (2003). Utilization of AcylHomoserine Lactone Quorum Signals for Growth by a Soil Pseudomonad and Pseudomonas aeruginosa PAO1. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 69(10), 5941–5949. https://doi.org/10.1128/AEM.69.10.5941
dcterms.referencesHuang, J., Shi, Y., Zeng, G., Gu, Y., & Chen, G. (2016). Acyl-homoserine lactone-based quorum sensing and quorum quenching hold promise to determine the performance of biological wastewater treatments : An overview. Chemosphere, 157, 137–151. https://doi.org/10.1016/j.chemosphere.2016.05.032
dcterms.referencesHuang, S. Y., & Zou, X. (2010). Advances and challenges in Protein-ligand docking. International Journal of Molecular Sciences, 11(8), 3016–3034. https://doi.org/10.3390/ijms11083016
dcterms.referencesHudaiberdiev, S., Choudhary, K. S., Vera Alvarez, R., Gelencsér, Z., Ligeti, B., Lamba, D., & Pongor, S. (2015). Census of solo LuxR genes in prokaryotic genomes. Frontiers in Cellular and Infection Microbiology, 5(March), 20. https://doi.org/10.3389/fcimb.2015.00020
dcterms.referencesHumphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics. https://doi.org/10.1016/0263- 7855(96)00018-5
dcterms.referencesJensen, F. (2007). Introduction to Computational Chemistry Computational Chemistry.
dcterms.referencesJones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997). Development and Validation of a Genetic Algorithm for Flexible Docking. Journal of Molecular Biology, 267(3), 727–748.
dcterms.referencesJorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926. https://doi.org/10.1063/1.445869
dcterms.referencesKalia, V. C., & Purohit, H. J. (2011). Quenching the quorum sensing system : potential antibacterial drug targets. Critical Reviews in Microbiology, 37(2), 121–140. https://doi.org/10.3109/1040841X.2010.532479
dcterms.referencesKiratisin, P., Tucker, K. D., & Passador, L. (2002). LasR , a Transcriptional Activator of Pseudomonas aeruginosa Virulence Genes , Functions as a Multimer LasR , a Transcriptional Activator of Pseudomonas aeruginosa Virulence Genes , Functions as a Multimer. Journal of Bacteriology, 184(17), 4912–4919. https://doi.org/10.1128/JB.184.17.4912
dcterms.referencesKoch, W., & Holthausen, M. C. (2001). A Chemist ’ s Guide to Density Functional Theory (2nd ed., Vol. 3).
dcterms.referencesKollef, M. H., Golan, Y., Micek, S. T., Shorr, A. F., & Restrepo, M. I. (2011). Appraising Contemporary Strategies to Combat Multidrug Resistant GramNegative Bacterial Infections – Proceedings and Data From the GramNegative Resistance Summit. Clinical Infectious Diseases 2011, 53, 33–55. https://doi.org/10.1093/cid/cir475
dcterms.referencesKOLLMAN, P., MASSOVA, I., REYES, C., KUHN, B., HUO, S., CHONG, L., … THOMAS, C. (2000). Calculating structures and free energies of complex molecules: Combing molecular mechanics and continuum models. Acc. Chem. Res., 33(12), 889–897.
dcterms.referencesKrom, B. P., Levy, N., Meijler, M. M., & Jabra-rizk, M. A. (2016). R e v i e w Farnesol and Candida albicans : Quorum Sensing or Not Quorum Sensing ? Israel Journal of Chemistry, 56, 295–301. https://doi.org/10.1002/ijch.201500025
dcterms.referencesLade, H., Paul, D., & Kweon, J. H. (2014a). N -Acyl Homoserine LactoneMediated Quorum Sensing with Special Reference to Use of Quorum Quenching Bacteria in Membrane Biofouling Control. BioMed Research International, 2014, 1–25.
dcterms.referencesLade, H., Paul, D., & Kweon, J. H. (2014b). Quorum Quenching Mediated Approaches for Control of Membrane Biofouling. International Journal of Biological Sciences, 10(5), 550–565. https://doi.org/10.7150/ijbs.9028
dcterms.referencesLamb, J. R., Patel, H., Montminy, T., Victoria, E., Iglewski, B. H., & Wagner, V. E. (2003). Functional Domains of the RhlR Transcriptional Regulator of Pseudomonas aeruginosa Functional Domains of the RhlR Transcriptional Regulator of Pseudomonas aeruginosa. Journal of Bacteriology, 185(24), 7129–7139. https://doi.org/10.1128/JB.185.24.7129
dcterms.referencesLandau, L., & Lifshitz, E. (1993). MECHANICS (3rd ed.).
dcterms.referencesLaSarre, B., & Federle, M. J. (2013). Exploiting Quorum Sensing To Confuse Bacterial Pathogens. Microbiology and Molecular Biology Reviews, 77(1), 73–111. https://doi.org/10.1128/MMBR.00046-12
dcterms.referencesLaue, B. E., Jiang, Y., Chhabra, S. R., Jacob, S., Stewart, G. S. A. B., Hardman, A., … Williams, P. (2000). The biocontrol strain Pseudomonas fluorescens F113 produces the Rhizobium small bacteriocin, N-(3-hydroxy7-cis-tetradecenoyl) homoserine lactone, via HdtS, a putative novel Nacylhomoserine lactone synthase. Microbiology, 146(10), 2469–2480. https://doi.org/10.1099/00221287-146-10-2469
dcterms.referencesLavecchia, A., & Di Giovanni, C. (2013). Virtual screening strategies in drug discovery: A critical review. Current Medicinal Chemistry, 20(23), 2839– 2860. https://doi.org/10.2174/09298673113209990001
dcterms.referencesLe-Thi-Thu, H., Casañola-Martín, G. M., Marrero-Ponce, Y., Rescigno, A., Abad, C., & Khan, M. T. H. (2014). A rational workflow for sequential virtual screening of chemical libraries on searching for new tyrosinase inhibitors. Current Topics in Medicinal Chemistry, 14(12), 1473–1485. Retrieved from http://www.scopus.com/inward/record.url?eid=2-s2.0- 84904016156&partnerID=tZOtx3y1
dcterms.referencesLeach, A. R. (2001). Molecular modelling _ principles and applications (Second). Prentice Hall.
dcterms.referencesLeach, A. R., Gillet, V. J., Lewis, R. A., & Taylor, R. (2010). Three-dimensional pharmacophore methods in drug discovery. Journal of Medicinal Chemistry, 53(2), 539–558. https://doi.org/10.1021/jm900817u
dcterms.referencesLeadbetter, J. R., & Greenberg, E. P. (2000). Metabolism of Acyl-Homoserine Lactone Quorum-Sensing Signals by Variovorax paradoxus. JOURNAL OF BACTERIOLOGY, 182(24), 6921–6926.
dcterms.referencesLee, J., & Zhang, L. (2015). The hierarchy quorum sensing network in Pseudomonas aeruginosa, 6(1), 26–41. ttps://doi.org/10.1007/s13238- 014-0100-x
dcterms.referencesLerat, E., & Moran, N. A. (2004). The Evolutionary History of Quorum-Sensing Systems in Bacteria. Molecular Biology and Evolution, 21(5), 903–913. https://doi.org/10.1093/molbev/msh097
dcterms.referencesLewis, K. (2007). Persister cells , dormancy and infectious disease. Nature Reviews Microbiology, 5(January), 48–56. https://doi.org/10.1038/nrmicro1557
dcterms.referencesLi, Z., & Nair, S. K. (2012). Quorum sensing: How bacteria can coordinate activity and synchronize their response to external signals? Protein Science, 21(10), 1403–1417. https://doi.org/10.1002/pro.2132
dcterms.referencesLindemann, A., Pessi, G., Schaefer, A. L., Mattmann, M. E., Christensen, Q. H., Kessler, A., … Harwood, C. S. (2011). Isovaleryl-homoserine lactone, an unusual branched-chain quorum-sensing signal from the soybean symbiont Bradyrhizobium japonicum. Proceedings of the National Academy of Sciences of the United States of America, 108(40), 16765–70. https://doi.org/10.1073/pnas.1114125108
dcterms.referencesLintz, M. J., Oinuma, K.-I., Wysoczynski, C. L., Greenberg, E. P., & Churchill, M. (2011). Crystal structure of QscR, a Pseudomonas aeruginosa quorum sensing signal receptor. Pnas, 108(38), 15763–15768. https://doi.org/10.1073/pnas.1112398108
dcterms.referencesLionta, E., Spyrou, G., Vassilatis, D. K., & Cournia, Z. (2014). Structure-Based Virtual Screening for Drug Discovery : Principles , Applications and Recent Advances. Current Topics in Medicinal Chemistry, 14, 1923–1938.
dcterms.referencesLipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23, 3–25
dcterms.referencesLipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2012). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings i. Advanced Drug Delivery Reviews, 64, 4–17. https://doi.org/10.1016/j.addr.2012.09.019
dcterms.referencesLou, Z. Q., Smyth, A. J., Gao, P., Qin, Y., & Farrand, S. K. (2003). Mutational analysis of TraR: Correlating function with molecular structure of a quorumsensing transcriptional activator. Journal of Biological Chemistry, 278(15), 13173–13182. https://doi.org/10.1074/jbc.M210035200
dcterms.referencesLu, Y., Shi, T., Wang, Y., Yang, H., Yan, X., Luo, X., … Zhu, W. (2009). Halogen Bonding s A Novel Interaction for Rational Drug Design ? Journal of Medicinal Chemistry, 52(9), 2854–2862.
dcterms.referencesMaddocks, S. E., & Oyston, P. C. F. (2008). Structure and function of the LysRtype transcriptional regulator ( LTTR ) family proteins. Microbiology, 154, 3609–3623. https://doi.org/10.1099/mic.0.2008/022772-0
dcterms.referencesMaldonado, A. G., Doucet, J. P., Petitjean, M., & Fan, B. T. (2006). Molecular similarity and diversity in chemoinformatics: From theory to applications. Molecular Diversity, 10(1), 39–79. https://doi.org/10.1007/s11030-006- 8697-1
dcterms.referencesMarkou, P., & Apidianakis, Y. (2014). Pathogenesis of intestinal Pseudomonas aeruginosa infection in patients with cancer PROMOTE THE PREVALENCE OF SOURCE OF SYSTEMIC AND REMOTE. Frontiers in Cellular and Infection Microbiology, 3(January), 1–5. https://doi.org/10.3389/fcimb.2013.00115
dcterms.referencesMashburn, L. M., & Whiteley, M. (2005). Membrane vesicles traffic signals and facilitate group activities in a prokaryote. Nature, 437(7057), 422–5. https://doi.org/10.1038/nature03925
dcterms.referencesMattmann, M. E., & Blackwell, H. E. (2010). Small molecules that modulate quorum sensing and control virulence in pseudomonas aeruginosa. Journal of Organic Chemistry, 75(20), 6737–6746. https://doi.org/10.1021/jo101237e
dcterms.referencesMedina-Franco, J. L., Fernández-de Gortaria, E., & Naveja, J. (2015). Química educación. Educación Química, 26, 180–186. https://doi.org/10.1016/j.eq.2015.05.002
dcterms.referencesMiller, B. R., McGee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314– 3321. https://doi.org/10.1021/ct300418h
dcterms.referencesMiller, B. R., McGee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314– 3321. https://doi.org/10.1021/ct300418h
dcterms.referencesMishra, V., Kashyap, S., & Hasija, Y. (2015). ScienceDirect Ligand based virtual screening for identifying potent inhibitors against viral neuraminidase: An in silico approach. Integrative Medicine Research, 9(1), 20–26. https://doi.org/10.1016/j.jtusci.2014.04.007
dcterms.referencesMOE. (2009). (Molecular Operating Environment). Scientific Computing & Instrumentation. Retrieved from http://www.chemcomp.com/index.htm
dcterms.referencesMontalvo-Acosta, J. J., & Cecchini, M. (2016). Computational Approaches to the Chemical Equilibrium Constant in Protein-ligand Binding. Molecular Informatics, 35(11–12), 555–567. https://doi.org/10.1002/minf.201600052 Moore, J. D., Gerdt, J. P., Eibergen, N. R., & Blackwell, H. E. (2014). Active
dcterms.referencesMoore, J. D., Gerdt, J. P., Eibergen, N. R., & Blackwell, H. E. (2014). Active efflux influences the potency of quorum sensing inhibitors in pseudomonas aeruginosa. ChemBioChem, 15(3), 435–442. https://doi.org/10.1002/cbic.201300701
dcterms.referencesMorris, G., & Huey, R. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem, 30(16), 2785– 2791. https://doi.org/10.1002/jcc.21256.AutoDock4
dcterms.referencesNealson, K. H., Platt, T., & Hastings, J. W. (1970). Cellular control of the synthesis and activity of the bacterial luminescent system. Journal of Bacteriology, 104(1), 313–322.
dcterms.referencesO’Brien, K. T., Noto, J. G., Nichols-O’Neill, L., & Perez, L. J. (2015). Potent irreversible inhibitors of LasR quorum sensing in Pseudomonas aeruginosa. ACS Medicinal Chemistry Letters, 6(2), 162–167. https://doi.org/10.1021/ml500459f
dcterms.referencesO’Reilly, M. C., & Blackwell, H. E. (2016). Structure-Based Design and Biological Evaluation of Triphenyl Scaffold-Based Hybrid Compounds as Hydrolytically Stable Modulators of a LuxR-Type Quorum Sensing Receptor. ACS Infectious Diseases, 2(1), 32–38. https://doi.org/10.1021/acsinfecdis.5b00112
dcterms.referencesPalmer, A. G., Streng, E., & Blackwell, H. E. (2011). Attenuation of virulence in pathogenic bacteria using synthetic quorum-sensing modulators under native conditions on plant hosts. ACS Chemical Biology, 6(12), 1348–56. https://doi.org/10.1021/cb200298g
dcterms.referencesParr, R. G., & Yang, W. (1989). Density-Functional Theory of Atoms andMolecules. (O. U. Press, Ed.). New York.
dcterms.referencesParsek, M. R., Val, D. L., Hanzelka, B. L., Cronan, J. E., & Greenberg, E. P. (1999). Acyl homoserine-lactone quorum-sensing signal generation. Proceedings of the National Academy of Sciences of the United States of America, 96(8), 4360–5. https://doi.org/10.1073/pnas.96.8.4360
dcterms.referencesQing, X., Xiao, Y. L., De Raeymaeker, J., Tame, RH, J., Zhang, K., De Maeyer, M., & Arnout, V. (2014). Pharmacophore modeling : advances , limitations , and current utility in drug discovery. Journal of Receptor, Ligand and Channel Research, 7, 81–92.
dcterms.referencesRampioni, G., Leoni, L., & Williams, P. (2014). Bioorganic Chemistry The art of antibacterial warfare : Deception through interference with quorum sensing – mediated communication. BIOORGANIC CHEMISTRY, 55, 60–68. https://doi.org/10.1016/j.bioorg.2014.04.005
dcterms.referencesRarey, M., Kramer, B., Lengauer, T., & Klebe, G. (1996). A Fast Flexible Docking Method using an Incremental Construction Algorithm. Journal of Molecular Biology, 261(3), 470–489.
dcterms.referencesRasmussen, T. B., & Givskov, M. (2006). Quorum-sensing inhibitors as antipathogenic drugs. International Journal of Medical Microbiology, 296, 149– 161. https://doi.org/10.1016/j.ijmm.2006.02.005
dcterms.referencesRipphausen, P., Nisius, B., & Bajorath, J. (2011). State-of-the-art in ligandbased virtual screening. FEATURES Drug Discovery Today, 16(May), 372– 376. https://doi.org/10.1016/j.drudis.2011.02.011
dcterms.referencesRojas-Badía, M. M. (2011). Quorum sensing in beneficial plant-bacteria associations. Revista Colombiana de Biotecnologia, 13(2), 135–143.
dcterms.referencesRumbaugh, K. P. (2011). Quorum Sensing Methods and Protocols. Methods in molecular biology (Clifton, N.J.) ; v. 692. 1064-3745. https://doi.org/10.1007/s13398-014-0173-7.2
dcterms.referencesRutherford, S., & Bassler, B. (2012). Bacterial Quorum Sensing : Its Role in Virulence and Possibilities for Its Control. Cold Spring Harbor Laboratory Press, 1–26.
dcterms.referencesRutherford, 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(11), 1–25. https://doi.org/10.1101/cshperspect.a012427
dcterms.referencesRyckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. https://doi.org/10.1016/0021-9991(77)90098-5
dcterms.referencesSadikot, R. T., Blackwell, T. S., Christman, J. W., & Prince, A. S. (2005). Pathogen – Host Interactions in Pseudomonas aeruginosa Pneumonia RESPIRATORY INFECTIONS. American Journal of Respiratory and Critical Care Medicine, 171(11), 1209–1223. https://doi.org/10.1164/rccm.200408-1044SO
dcterms.referencesSaldívar-gonzález, F., & Medina-franco, F. D. P. J. L. (2017). Descubrimiento y desarrollo de fármacos: un enfoque computacional. Educación Química, 28(1), 51–58. https://doi.org/10.1016/j.eq.2016.06.002
dcterms.referencesSchaefer, A. L., Greenberg, E. P., Oliver, C. M., Oda, Y., Huang, J. J., BittanBanin, G., … Harwood, C. S. (2008). A new class of homoserine lactone quorum-sensing signals. Nature, 454(7204), 595–599. https://doi.org/10.1038/nature07088
dcterms.referencesSchneider, G., & Fechner, U. (2005). Computer-based de novo design of druglike molecules. Nature Reviews Drug Discovery, 4(8), 649–663. https://doi.org/10.1038/nrd1799
dcterms.referencesSchuster, M., Sexton, D. J., Diggle, S. P., & Greenberg, E. P. (2013). Acylhomoserine lactone quorum sensing: from evolution to application. Annual Review of Microbiology, 67(May 2013), 43–63. https://doi.org/10.1146/annurev-micro-092412-155635
dcterms.referencesScreening, H., Borlee, B. R., Geske, G. D., Blackwell, H. E., & Handelsman, J. (2010). Identification of Synthetic Inducers and Inhibitors of the QuorumSensing Regulator LasR in Pseudomonas aeruginosa by. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 76(24), 8255–8258. https://doi.org/10.1128/AEM.00499-10
dcterms.referencesSen, S., Farooqui, N. A., Easwari, T. S., & Roy, B. (2012). CoMFA -3D QSAR APPROCH IN DRUG DESIGN. International Journal of Research and Development in Pharmacy and Life Sciences, 1(4), 167–175.
dcterms.referencesSheridan, R. P., & Kearsley, S. K. (2002). Why do we need so many chemical simialrity search methods? Ddt, 7(17), 903–911.
dcterms.referencesSherrill, D. (2000). An Introduction to Hartree-Fock Molecular Orbital Theory What. Georgia Inst. of Technology, 1–8.
dcterms.referencesSippl, W. (2000). Receptor-based 3D QSAR analysis of estrogen receptor ligands – merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods ∗. Journal of ComputerAided Molecular Design, 14, 559–572.
dcterms.referencesSmith, R. S., & Iglewski, B. H. (2003). Pseudomonas aeruginosa quorum sensing as a potential antimicrobial target. Journal of Clinical Investigation, 112(10), 1460–1465. https://doi.org/10.1172/JCI200320364
dcterms.referencesSoulère, L., Frezza, M., Queneau, Y., & Doutheau, A. (2007). Exploring the active site of acyl homoserine lactones-dependent transcriptional regulators with bacterial quorum sensing modulators using molecular mechanics and docking studies. Journal of Molecular Graphics and Modelling, 26(2), 581– 590. https://doi.org/10.1016/j.jmgm.2007.04.004
dcterms.referencesSoulère, L., Sabbah, M., Fontaine, F., Queneau, Y., & Doutheau, A. (2010). LuxR-dependent quorum sensing: Computer aided discovery of new inhibitors structurally unrelated to N-acylhomoserine lactones. Bioorganic and Medicinal Chemistry Letters, 20(15), 4355–4358. https://doi.org/10.1016/j.bmcl.2010.06.081
dcterms.referencesStevens, A. M., Dolan, K. M., & Greenberg, E. P. (1994). Synergistic binding of the Vibrio fischeri LuxR transcriptional activator domain and RNA polymerase to the lux promoter region. Proceedings of the National Academy of Sciences of the United States of America, 91(26), 12619– 12623. https://doi.org/10.1073/pnas.92.8.3631a
dcterms.referencesStewart, J. J. P. (1989). Optimization of Parameters for Semiempirical Methods .2. Applications. J. Comput. Chem., 10(2), 221–264. https://doi.org/10.1002/jcc.540100209
dcterms.referencesStewart, J. J. P. (2013). Optimization of parameters for semiempirical methods VI : more modifications to the NDDO approximations and re-optimization of parameters. J Mol Model, 19, 1–32. https://doi.org/10.1007/s00894-012- 1667-x
dcterms.referencesStumpfe, D., & Bajorath, J. (2011). Similarity searching. Computational Molecular Science, 1(April), 260–282. https://doi.org/10.1002/wcms.23
dcterms.referencesStumpfe, D., & Bajorath, J. (2012). Exploring activity cliffs in medicinal chemistry. Journal of Medicinal Chemistry, 55(7), 2932–2942. https://doi.org/10.1021/jm201706b
dcterms.referencesStumpfe, D., León, A. de, Dimova, D., & Bajorath, J. (2014). Follow up: Advancing the activity cliff concept, part II ANRT biblio Chemistry ML NeuralNets QSAR. F1000Research, 199, 1–11. https://doi.org/10.12688/f1000research.3788.1
dcterms.referencesSuneby, E. G., Herndon, L. R., & Schneider, T. L. (2017). Pseudomonas aeruginosa LasR·DNA Binding Is Directly Inhibited by Quorum Sensing Antagonists. ACS Infectious Diseases, acsinfecdis.6b00163. https://doi.org/10.1021/acsinfecdis.6b00163
dcterms.referencesThiel, V., Kunze, B., Verma, P., Wagner-Döbler, I., & Schulz, S. (2009). New structural variants of homoserine lactones in bacteria. ChemBioChem, 10(11), 1861–1868. https://doi.org/10.1002/cbic.200900126
dcterms.referencesTian, S., Wang, J., Li, Y., Xu, X., & Hou, T. (2012). Drug-likeness analysis of traditional chinese medicines: Prediction of drug-likeness using machine learning approaches. Molecular Pharmaceutics, 9(10), 2875–2886. https://doi.org/10.1021/mp300198d
dcterms.referencesTodeschini, R., & Consonni, V. (2009). Chemometrics in QSAR. Comprehensive Chemometrics, 4, 129–172.
dcterms.referencesTomasz, A. (1965). Control of the competent state in Pneumococcus by a hormone-like cell product. Nature, 208(5006), 155–159. https://doi.org/10.1038/208155a0
dcterms.referencesTurner, K. H., Everett, J., Trivedi, U., Rumbaugh, K. P., & Whiteley, M. (2014). Requirements for Pseudomonas aeruginosa Acute Burn and Chronic Surgical Wound Infection. PLOS Genetics, 10(7), 1–12. https://doi.org/10.1371/journal.pgen.1004518
dcterms.referencesTurner, K. H., Wessel, A. K., Palmer, G. C., Murray, J. L., & Whiteley, M. (2015). Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum. Proceedings of the National Academy of Sciences of the United States of America, 112(13), 4110–5. https://doi.org/10.1073/pnas.1419677112
dcterms.referencesVannini, A., Volpari, C., Gargioli, C., Muraglia, E., Cortese, R., De Francesco, 102 R., … Di Marco, S. (2002). The crystal structure of the quorum sensing protein TraR bound to its autoinducer and target DNA. EMBO Journal, 21(17), 4393–4401. https://doi.org/10.1093/emboj/cdf459
dcterms.referencesVistoli, G., Pedretti, A., & Testa, B. (2008). Assessing drug-likeness - what are we missing? Drug Discovery Today, 13(7–8), 285–294. https://doi.org/10.1016/j.drudis.2007.11.007
dcterms.referencesVyas, V., Jain, A., Jain, A., & Gupta, A. (2008). Virtual screening: A fast tool for drug design. Scientia Pharmaceutica, 76(3), 333–360. https://doi.org/10.3797/scipharm.0803-03
dcterms.referencesWalters, W. P., & Murcko, M. A. (2002). Prediction of “drug-likeness.” Advanced Drug Delivery Reviews, 54(3), 255–271. https://doi.org/10.1016/S0169- 409X(02)00003-0
dcterms.referencesWang, J. M., Wolf, R. M., Caldwell, J. W., Kollman, P. a, & Case, D. a. (2004). Development and testing of a general amber force field. J. Comput. Chem., 25(9), 1157–1174. https://doi.org/10.1002/jcc.20035
dcterms.referencesWarren, G. L., Andrews, C. V, Capelli, a, Clarke, B., LaLonde, J., Lambert, M. H., … Head, M. S. (2006). A critical assessment of docking programs and scoring functions.Capelli, A.LaLonde, J.Semus, S. F.Head, M. S. J. Med. Chem., (49), 5912–5931.
dcterms.referencesWaters, C. M., & Bassler, B. L. (2005). Quorum Sensing : Cell-to-Cell Communication in Bacteria. Annual Reviews in Cell Development Biology, 21(1), 319–346. https://doi.org/10.1146/annurev.cellbio.21.012704.131001
dcterms.referencesWatson, W. T., Minogue, T. D., Val, D. L., von Bodman, S. B., & Churchill, M. E. a. (2002). Structural basis and specificity of acyl-homoserine lactone signal production in bacterial quorum sensing. Molecular Cell, 9(3), 685–694. https://doi.org/10.1016/S1097-2765(02)00480-X
dcterms.referencesWelsh, M. A., & Blackwell, H. E. (2016a). Chemical Genetics Reveals Environment-Specific Roles for Quorum Sensing Circuits in Pseudomonas aeruginosa. Cell Chemical Biology, 23(3), 361–369. https://doi.org/10.1016/j.chembiol.2016.01.006
dcterms.referencesWelsh, M. A., & Blackwell, H. E. (2016b). Chemical probes of quorum sensing: from compound development to biological discovery. FEMS Microbiology Reviews, 40(5), 774–794. https://doi.org/10.1093/femsre/fuw009
dcterms.referencesWermuth, C. G., Ganellin, C. R., Lindberg, P., & Mitscher, L. A. (1998). GLOSSARY OF TERMS USED IN MEDICINAL CHEMISTRY. Pure Appl. Chem, 70(5), 1129–1143
dcterms.referencesWilliams, P., Winzer, K., Chan, W. C., & Cámara, M. (2007). Look who’s talking: communication and quorum sensing in the bacterial world. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 362(1483), 1119–1134. https://doi.org/10.1098/rstb.2007.2039
dcterms.referencesWinzer, K., Hardie, K. R., & Williams, P. (2002). Bacterial cell-to-cell communication : sorry , can ’ t talk now — gone to lunch ! Bacterial Cell-toCell Communication, 5, 216–222.
dcterms.referencesXu, X., & Goddard, W. A. (2004). The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties. Proceedings of the National Academy of Sciences of the United States of America, 101(9), 2673–2677. https://doi.org/10.1073/pnas.0308730100
dcterms.referencesYao, Y., Martinez-Yamout, M. A., Dickerson, T. J., Brogan, A. P., Wright, P. E., & Dyson, H. J. (2006). Structure of the Escherichia coli quorum sensing protein SdiA: Activation of the folding switch by acyl homoserine lactones. Journal of Molecular Biology, 355(2), 262–273. https://doi.org/10.1016/j.jmb.2005.10.041
dcterms.referencesYates, E. A., Philipp, B., Buckley, C., Atkinson, S., Chhabra, S. R., Sockett, R. E., … Dessaux, Y. (2002). N -Acylhomoserine Lactones Undergo Lactonolysis in a pH- , Temperature- , and Acyl Chain Length-Dependent Manner during Growth of Yersinia pseudotuberculosis and Pseudomonas aeruginosa. INFECTION AND IMMUNITY, 70(10), 5635–5646. https://doi.org/10.1128/IAI.70.10.5635
dcterms.referencesYoung, D. C. (2001). COMPUTATIONAL CHEMISTRY A Practical Guide for Applying Techniques to Real-World Problems. New York (Vol. 9). https://doi.org/10.1002/jat.1666
dcterms.referencesZheng, Y., & Sintim, H. O. (2014). Molecular insights into how ligands activate or inactivate LasR. Chemistry and Biology, 21(10), 1261–1263. https://doi.org/10.1016/j.chembiol.2014.10.001
dcterms.referencesZhu, T., Cao, S., Su, P.-C., Patel, R., Shah, D., Chokshi, H. B., … Johnson, M. E. (2013). Practical, Hit Identification and Optimization in Virtual Screening: Analysis, Recommendations Based Upon a Critical Literature. Journal of Medicinal Chemistry, 56(17), 6560–6572. https://doi.org/10.1021/jm301916b.Hit
dcterms.referencesZou, Y., & Nair, S. K. (2009a). Molecular Basis for the Recognition of Structurally Distinct Autoinducer Mimics by the Pseudomonas aeruginosa LasR Quorum-Sensing Signaling Receptor. Chemistry and Biology, 16(9), 961–970. https://doi.org/10.1016/j.chembiol.2009.09.001
dcterms.referencesZou, Y., & Nair, S. K. (2009b). Molecular Basis for the Recognition of Structurally Distinct Autoinducer Mimics by the Pseudomonas aeruginosa LasR Quorum-Sensing Signaling Receptor. Chemistry and Biology, 16(9), 961–970. https://doi.org/10.1016/j.chembiol.2009.09.001
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https://creativecommons.org/licenses/by-nc-nd/4.0
Excepto si se señala otra cosa, la licencia del ítem se describe como https://creativecommons.org/licenses/by-nc-nd/4.0