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Modelado molecular de análogos estructurales de las Acil homoserina lactonas en el sitio activo del receptor Lasr
dc.contributor.advisor | Vivas Reyes, Ricardo (Director/a) | |
dc.contributor.advisor | Alí Torres, Jorge Isaac (Director/a) | |
dc.contributor.advisor | Zapata Rivera, Jhon (Director/a) | |
dc.contributor.author | Ahumedo Monterrosa, Maicol José | |
dc.date.accessioned | 2020-03-13T14:22:00Z | |
dc.date.available | 2020-03-13T14:22:00Z | |
dc.date.issued | 2018 | |
dc.identifier.citation | TD541.28 / A86 | es |
dc.identifier.uri | https://hdl.handle.net/11227/10030 | |
dc.identifier.uri | http://dx.doi.org/10.57799/11227/79 | |
dc.description | Tesis (Doctor en Ciencias). -- Universidad de Cartagena. Facultad de Ciencias Exactas y Naturales, 2018 | es |
dc.description.abstract | En 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 aeruginosa | es |
dc.format.medium | application/pdf | |
dc.language.iso | spa | es |
dc.publisher | Universidad de Cartagena | es |
dc.rights.uri | https://creativecommons.org/licenses/by-nc-nd/4.0 | |
dc.subject | Estructura molecular | es |
dc.subject | Química cuántica | es |
dc.subject | Química | es |
dc.title | Modelado molecular de análogos estructurales de las Acil homoserina lactonas en el sitio activo del receptor Lasr | es |
dc.type | Trabajo de grado - Doctorado | spa |
dcterms.references | Abagyan, 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.references | Adcock, 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.references | Ahlgren, 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.references | Ahumedo, 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.references | Ahumedo, 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.references | Ahumedo, 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.references | Alberto, G., & Rossello, M. (2013). Quorum sensing en bacterias y levaduras. Medicina Clinica, 141(8), 353–357. | |
dcterms.references | Amara, 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.references | Atkinson, 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.references | Auffinger, P., Hays, F. A., Westhof, E., & Ho, P. S. (2004). Halogen bonds in biological molecules. Proc. Natl. Acad. Sci., 101(48), 16789–16794. | |
dcterms.references | Bai, 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.references | Bassler, B. L., & Losick, R. (2006). Bacterially Speaking. Cell, 125(2), 237–246. https://doi.org/10.1016/j.cell.2006.04.001 | |
dcterms.references | Bassler, 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.references | Bayly, 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.references | Bhargava, 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.references | Blackwell, 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.references | Blankenship, 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.references | Bonomo, R. A., & Szabo, D. (2006). Mechanisms of Multidrug Resistance in Acinetobacter Species and Pseudomonas aeruginosa. Clinical Infectious Diseases, 44106, 49–56. | |
dcterms.references | Bottomley, 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.references | Boucher, 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.references | Brown, 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.references | Burton, 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.references | Cai, 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.references | Camilli, A., & Bassler, B. . (2006). NIH Public Access. Nature Reviews. Microbiology, 311(5764), 1113–1116. https://doi.org/10.1126/science.1121357.Bacterial | |
dcterms.references | Cavasotto, C. (2016). In Silico drug Discovery and Design Theory, Methods, Challenges, and Applications. | |
dcterms.references | Cegelski, L., Marshall, G. R., Eldridge, G. R., & Hultgren, S. J. (2008). NIH Public Access. Nat Rev Microbiol, 6(1), 17–27. | |
dcterms.references | Cereto-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.references | Chakrabarti, 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.references | Chen, 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.references | Cheng, 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.references | Chipot, 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.references | Cho, 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.references | Christensen, 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.references | Churchill, M. E. A., & Chen, L. (2011). NIH Public Access (Vol. 111). https://doi.org/10.1021/cr1000817.Structural | |
dcterms.references | Cramer, C. J. (2004). Essentials of Computational Chemistry Theories and Models. New York (Second Edi). https://doi.org/10.1037/023990 | |
dcterms.references | Cramer, 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.references | Crousilles, 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.references | Cuevas, G., & Cortés, F. (2003). Introducción a la Química Computacional. | |
dcterms.references | Danishuddin, 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.references | de 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.references | Dekimpe, 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.references | Dennington, R., Keith, T., & Millam, J. (2009). GaussView. Semichem Inc., Shawnee Mission KS. | |
dcterms.references | Dong, 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.references | Donlan, 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.references | Doshi, 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.references | Duan, 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.references | Eberhard, 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.references | Folkesson, 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.references | Frei, 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.references | Friesner, 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.references | Frisch, 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.references | Frisch, J. B., & Foresman, A. (1994). Exploring_Chemistry_With_Electronic_Structure_Methods. | |
dcterms.references | Fuqua, 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.references | Fuqua, 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.references | Galloway, 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.references | Galloway, 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.references | Genheden, 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.references | Gerdt, 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.references | Gerdt, 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.references | Gerdt, 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.references | Geske, 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.references | Geske, 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.references | Geske, 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.references | Godbout, 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.references | González, 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.references | Goodisman, J. (1973). Diatomic interaction potential theory. Academic Press, 1. | |
dcterms.references | Gould, 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.references | Gutiérres-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.references | Hanzelka, 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.references | Hartmann, 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.references | Henke, 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.references | Hense, 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.references | Hentzer, 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.references | Hentzer, 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.references | HETÉNYI, 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.references | Homeyer, 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.references | Homeyer, 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.references | Huang, 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.references | Huang, 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.references | Huang, 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.references | Hudaiberdiev, 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.references | Humphrey, 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.references | Jensen, F. (2007). Introduction to Computational Chemistry Computational Chemistry. | |
dcterms.references | Jones, 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.references | Jorgensen, 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.references | Kalia, 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.references | Kiratisin, 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.references | Koch, W., & Holthausen, M. C. (2001). A Chemist ’ s Guide to Density Functional Theory (2nd ed., Vol. 3). | |
dcterms.references | Kollef, 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.references | KOLLMAN, 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.references | Krom, 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.references | Lade, 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.references | Lade, 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.references | Lamb, 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.references | Landau, L., & Lifshitz, E. (1993). MECHANICS (3rd ed.). | |
dcterms.references | LaSarre, 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.references | Laue, 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.references | Lavecchia, 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.references | Le-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.references | Leach, A. R. (2001). Molecular modelling _ principles and applications (Second). Prentice Hall. | |
dcterms.references | Leach, 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.references | Leadbetter, 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.references | Lee, 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.references | Lerat, 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.references | Lewis, K. (2007). Persister cells , dormancy and infectious disease. Nature Reviews Microbiology, 5(January), 48–56. https://doi.org/10.1038/nrmicro1557 | |
dcterms.references | Li, 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.references | Lindemann, 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.references | Lintz, 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.references | Lionta, 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.references | Lipinski, 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.references | Lipinski, 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.references | Lou, 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.references | Lu, 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.references | Maddocks, 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.references | Maldonado, 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.references | Markou, 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.references | Mashburn, 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.references | Mattmann, 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.references | Medina-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.references | Miller, 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.references | Milton, 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.references | Mishra, 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.references | MOE. (2009). (Molecular Operating Environment). Scientific Computing & Instrumentation. Retrieved from http://www.chemcomp.com/index.htm | |
dcterms.references | Montalvo-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.references | Moore, 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.references | Morris, 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.references | Nealson, 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.references | O’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.references | O’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.references | O’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.references | Palmer, 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.references | Parr, R. G., & Yang, W. (1989). Density-Functional Theory of Atoms andMolecules. (O. U. Press, Ed.). New York. | |
dcterms.references | Parsek, 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.references | Qing, 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.references | Rampioni, 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.references | Rarey, 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.references | Rasmussen, 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.references | Ripphausen, 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.references | Rojas-Badía, M. M. (2011). Quorum sensing in beneficial plant-bacteria associations. Revista Colombiana de Biotecnologia, 13(2), 135–143. | |
dcterms.references | Rumbaugh, 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.references | Rutherford, S., & Bassler, B. (2012). Bacterial Quorum Sensing : Its Role in Virulence and Possibilities for Its Control. Cold Spring Harbor Laboratory Press, 1–26. | |
dcterms.references | Rutherford, S. T., & Bassler, B. L. (2012). Bacterial quorum sensing: its role in virulence and possibilities for its control. Cold Spring Harbor Perspectives in Medicine, 2(11), 1–25. https://doi.org/10.1101/cshperspect.a012427 | |
dcterms.references | Ryckaert, 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.references | Sadikot, 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.references | Saldívar-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.references | Schaefer, 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.references | Schneider, 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.references | Schuster, 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.references | Screening, 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.references | Sen, 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.references | Sheridan, R. P., & Kearsley, S. K. (2002). Why do we need so many chemical simialrity search methods? Ddt, 7(17), 903–911. | |
dcterms.references | Sherrill, D. (2000). An Introduction to Hartree-Fock Molecular Orbital Theory What. Georgia Inst. of Technology, 1–8. | |
dcterms.references | Sippl, 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.references | Smith, 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.references | Soulère, 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.references | Soulère, 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.references | Stevens, 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.references | Stewart, 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.references | Stewart, 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.references | Stumpfe, D., & Bajorath, J. (2011). Similarity searching. Computational Molecular Science, 1(April), 260–282. https://doi.org/10.1002/wcms.23 | |
dcterms.references | Stumpfe, 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.references | Stumpfe, 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.references | Suneby, 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.references | Thiel, 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.references | Tian, 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.references | Todeschini, R., & Consonni, V. (2009). Chemometrics in QSAR. Comprehensive Chemometrics, 4, 129–172 | |
dcterms.references | Tomasz, 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.references | Turner, 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.references | Turner, 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.references | Vannini, 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.references | Vistoli, 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.references | Vyas, 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.references | Walters, 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.references | Wang, 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.references | Warren, 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.references | Waters, 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.references | Watson, 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.references | Welsh, 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.references | Welsh, 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.references | Wermuth, 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.references | Williams, 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.references | Winzer, 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.references | Xu, 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.references | Yao, 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.references | Yates, 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.references | Young, 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.references | Zheng, 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.references | Zhu, 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.references | Zou, 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.references | Zou, 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.references | Abagyan, 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.references | Adcock, 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.references | Ahlgren, 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.references | Ahumedo, 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.references | Ahumedo, 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.references | Ahumedo, 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.references | Alberto, G., & Rossello, M. (2013). Quorum sensing en bacterias y levaduras. Medicina Clinica, 141(8), 353–357. | |
dcterms.references | Amara, 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.references | Atkinson, 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.references | Auffinger, P., Hays, F. A., Westhof, E., & Ho, P. S. (2004). Halogen bonds in biological molecules. Proc. Natl. Acad. Sci., 101(48), 16789–16794. | |
dcterms.references | Bai, 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.references | Bassler, B. L., & Losick, R. (2006). Bacterially Speaking. Cell, 125(2), 237–246. https://doi.org/10.1016/j.cell.2006.04.001 | |
dcterms.references | Bassler, 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.references | Bayly, 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.references | Bhargava, 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.references | Blackwell, 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.references | Blankenship, 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.references | Bonomo, R. A., & Szabo, D. (2006). Mechanisms of Multidrug Resistance in Acinetobacter Species and Pseudomonas aeruginosa. Clinical Infectious Diseases, 44106, 49–56. | |
dcterms.references | Bottomley, 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.references | Boucher, 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.references | Brown, 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.references | Burton, 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.references | Cai, 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.references | Camilli, A., & Bassler, B. . (2006). NIH Public Access. Nature Reviews. Microbiology, 311(5764), 1113–1116. https://doi.org/10.1126/science.1121357.Bacterial | |
dcterms.references | Capilato, 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.references | Case, 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.references | Cavasotto, C. (2016). In Silico drug Discovery and Design Theory, Methods, Challenges, and Applications. | |
dcterms.references | Cegelski, L., Marshall, G. R., Eldridge, G. R., & Hultgren, S. J. (2008). NIH Public Access. Nat Rev Microbiol, 6(1), 17–27. | |
dcterms.references | Cereto-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.references | Chakrabarti, 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.references | Chen, 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.references | Cheng, 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.references | Chipot, 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.references | Cho, 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.references | Christensen, 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.references | Churchill, M. E. A., & Chen, L. (2011). NIH Public Access (Vol. 111). https://doi.org/10.1021/cr1000817.Structural | |
dcterms.references | Cramer, C. J. (2004). Essentials of Computational Chemistry Theories and Models. New York (Second Edi). https://doi.org/10.1037/023990 | |
dcterms.references | Cramer, 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.references | Crousilles, 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.references | Cuevas, G., & Cortés, F. (2003). Introducción a la Química Computacional. | |
dcterms.references | Danishuddin, 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.references | de 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.references | Dekimpe, 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.references | Dennington, R., Keith, T., & Millam, J. (2009). GaussView. Semichem Inc., Shawnee Mission KS. | |
dcterms.references | Ding, 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.references | Dong, 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.references | Donlan, 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.references | Doshi, 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.references | Duan, 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.references | Eberhard, 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.references | Folkesson, 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.references | Frei, 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.references | Friesner, 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.references | Frisch, 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.references | Frisch, J. B., & Foresman, A. (1994). Exploring_Chemistry_With_Electronic_Structure_Methods. | |
dcterms.references | Fuqua, 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.references | Fuqua, 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.references | Galloway, 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.references | Galloway, 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.references | Genheden, 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.references | Genheden, 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.references | Gerdt, 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.references | Geske, 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.references | Geske, 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.references | Geske, 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.references | Godbout, 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.references | González, 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.references | Goodisman, J. (1973). Diatomic interaction potential theory. Academic Press, 1. | |
dcterms.references | Gould, 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.references | Gutiérres-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.references | Hanzelka, 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.references | Hartmann, 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.references | Henke, 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.references | Hense, 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.references | Hentzer, 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.references | Hentzer, 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.references | HETÉNYI, 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.references | Homeyer, 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.references | Homeyer, 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.references | Huang, 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.references | Huang, 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.references | Huang, 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.references | Hudaiberdiev, 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.references | Humphrey, 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.references | Jensen, F. (2007). Introduction to Computational Chemistry Computational Chemistry. | |
dcterms.references | Jones, 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.references | Jorgensen, 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.references | Kalia, 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.references | Kiratisin, 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.references | Koch, W., & Holthausen, M. C. (2001). A Chemist ’ s Guide to Density Functional Theory (2nd ed., Vol. 3). | |
dcterms.references | Kollef, 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.references | KOLLMAN, 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.references | Krom, 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.references | Lade, 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.references | Lade, 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.references | Lamb, 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.references | Landau, L., & Lifshitz, E. (1993). MECHANICS (3rd ed.). | |
dcterms.references | LaSarre, 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.references | Laue, 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.references | Lavecchia, 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.references | Le-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.references | Leach, A. R. (2001). Molecular modelling _ principles and applications (Second). Prentice Hall. | |
dcterms.references | Leach, 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.references | Leadbetter, 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.references | Lee, 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.references | Lerat, 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.references | Lewis, K. (2007). Persister cells , dormancy and infectious disease. Nature Reviews Microbiology, 5(January), 48–56. https://doi.org/10.1038/nrmicro1557 | |
dcterms.references | Li, 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.references | Lindemann, 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.references | Lintz, 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.references | Lionta, 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.references | Lipinski, 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.references | Lipinski, 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.references | Lou, 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.references | Lu, 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.references | Maddocks, 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.references | Maldonado, 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.references | Markou, 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.references | Mashburn, 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.references | Mattmann, 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.references | Medina-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.references | Miller, 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.references | Miller, 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.references | Mishra, 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.references | MOE. (2009). (Molecular Operating Environment). Scientific Computing & Instrumentation. Retrieved from http://www.chemcomp.com/index.htm | |
dcterms.references | Montalvo-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.references | Moore, 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.references | Morris, 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.references | Nealson, 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.references | O’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.references | O’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.references | Palmer, 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.references | Parr, R. G., & Yang, W. (1989). Density-Functional Theory of Atoms andMolecules. (O. U. Press, Ed.). New York. | |
dcterms.references | Parsek, 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.references | Qing, 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.references | Rampioni, 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.references | Rarey, 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.references | Rasmussen, 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.references | Ripphausen, 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.references | Rojas-Badía, M. M. (2011). Quorum sensing in beneficial plant-bacteria associations. Revista Colombiana de Biotecnologia, 13(2), 135–143. | |
dcterms.references | Rumbaugh, 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.references | Rutherford, S., & Bassler, B. (2012). Bacterial Quorum Sensing : Its Role in Virulence and Possibilities for Its Control. Cold Spring Harbor Laboratory Press, 1–26. | |
dcterms.references | Rutherford, S. T., & Bassler, B. L. (2012). Bacterial quorum sensing: its role in virulence and possibilities for its control. Cold Spring Harbor Perspectives in Medicine, 2(11), 1–25. https://doi.org/10.1101/cshperspect.a012427 | |
dcterms.references | Ryckaert, 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.references | Sadikot, 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.references | Saldívar-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.references | Schaefer, 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.references | Schneider, 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.references | Schuster, 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.references | Screening, 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.references | Sen, 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.references | Sheridan, R. P., & Kearsley, S. K. (2002). Why do we need so many chemical simialrity search methods? Ddt, 7(17), 903–911. | |
dcterms.references | Sherrill, D. (2000). An Introduction to Hartree-Fock Molecular Orbital Theory What. Georgia Inst. of Technology, 1–8. | |
dcterms.references | Sippl, 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.references | Smith, 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.references | Soulère, 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.references | Soulère, 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.references | Stevens, 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.references | Stewart, 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.references | Stewart, 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.references | Stumpfe, D., & Bajorath, J. (2011). Similarity searching. Computational Molecular Science, 1(April), 260–282. https://doi.org/10.1002/wcms.23 | |
dcterms.references | Stumpfe, 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.references | Stumpfe, 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.references | Suneby, 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.references | Thiel, 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.references | Tian, 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.references | Todeschini, R., & Consonni, V. (2009). Chemometrics in QSAR. Comprehensive Chemometrics, 4, 129–172. | |
dcterms.references | Tomasz, 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.references | Turner, 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.references | Turner, 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.references | Vannini, 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.references | Vistoli, 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.references | Vyas, 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.references | Walters, 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.references | Wang, 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.references | Warren, 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.references | Waters, 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.references | Watson, 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.references | Welsh, 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.references | Welsh, 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.references | Wermuth, 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.references | Williams, 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.references | Winzer, 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.references | Xu, 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.references | Yao, 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.references | Yates, 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.references | Young, 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.references | Zheng, 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.references | Zhu, 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.references | Zou, 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.references | Zou, 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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