<?xml version="1.0" encoding="ISO-8859-1"?><article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<front>
<journal-meta>
<journal-id>0121-4004</journal-id>
<journal-title><![CDATA[Vitae]]></journal-title>
<abbrev-journal-title><![CDATA[Vitae]]></abbrev-journal-title>
<issn>0121-4004</issn>
<publisher>
<publisher-name><![CDATA[Facultad de Química Farmacéutica, Universidad de Antioquia]]></publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id>S0121-40042017000200089</article-id>
<article-id pub-id-type="doi">10.17533/udea.vitae.v24n2a02</article-id>
<title-group>
<article-title xml:lang="en"><![CDATA[VIRTUAL SCREENING: IDENTIFICATION OF COMPOUNDS WITH POSSIBLE QUORUM SENSING AGONISTIC ACTIVITY IN Pseudomonas aeruginosa]]></article-title>
<article-title xml:lang="es"><![CDATA[CRIBADO VIRTUAL: IDENTIFICACIÓN DE POSIBLES COMPUESTOS CON ACTIVIDAD MODULADORA DEL QUORUM SENSING EN Pseudomonas aeruginosa]]></article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Ahumedo]]></surname>
<given-names><![CDATA[Maicol]]></given-names>
</name>
<xref ref-type="aff" rid="Aff"/>
<xref ref-type="aff" rid="Aaf"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Velásquez]]></surname>
<given-names><![CDATA[Margarita]]></given-names>
</name>
<xref ref-type="aff" rid="Aff"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Reyes]]></surname>
<given-names><![CDATA[Ricardo Vivas]]></given-names>
</name>
<xref ref-type="aff" rid="Aff"/>
<xref ref-type="aff" rid="Aaf"/>
</contrib>
</contrib-group>
<aff id="Af1">
<institution><![CDATA[,Universidad de Cartagena Facultad de Ciencias Exactas y Naturales Programa de Química]]></institution>
<addr-line><![CDATA[Cartagena ]]></addr-line>
<country>Colombia</country>
</aff>
<aff id="Af2">
<institution><![CDATA[,Universidad de la Amazonia  ]]></institution>
<addr-line><![CDATA[Caquetá ]]></addr-line>
<country>Colombia</country>
</aff>
<aff id="Af3">
<institution><![CDATA[,Fundación Universitaria Tecnológico de Comfenalco  Programa de Ingeniería Industrial]]></institution>
<addr-line><![CDATA[Cartagena ]]></addr-line>
<country>Colombia</country>
</aff>
<pub-date pub-type="pub">
<day>00</day>
<month>08</month>
<year>2017</year>
</pub-date>
<pub-date pub-type="epub">
<day>00</day>
<month>08</month>
<year>2017</year>
</pub-date>
<volume>24</volume>
<numero>2</numero>
<fpage>89</fpage>
<lpage>101</lpage>
<copyright-statement/>
<copyright-year/>
<self-uri xlink:href="http://www.scielo.org.co/scielo.php?script=sci_arttext&amp;pid=S0121-40042017000200089&amp;lng=en&amp;nrm=iso"></self-uri><self-uri xlink:href="http://www.scielo.org.co/scielo.php?script=sci_abstract&amp;pid=S0121-40042017000200089&amp;lng=en&amp;nrm=iso"></self-uri><self-uri xlink:href="http://www.scielo.org.co/scielo.php?script=sci_pdf&amp;pid=S0121-40042017000200089&amp;lng=en&amp;nrm=iso"></self-uri><abstract abstract-type="short" xml:lang="en"><p><![CDATA[ABSTRACT  Background: Quorum sensing (QS) is a cell density dependent mechanism that allows bacteria to regulate the expression of specific genes in response to changes in their population density, thus controlling their activities in order to produce a response as a unit multicellular. These responses include production of virulence factors, formation of biofilm, bioluminescence, sporulation, among other behavior.  Objectives:  The objective of this work was to obtain pharmacophore models able to filter and identify molecules with possible agonist activity of uorum sensing and to find possible candidates based on calculations of molecular docking.  Methods:  The structure of the receptor was taken from the Protein Data Bank (PDB). The program AutoDock 4.2 was used to perform docking calculations. The 3D structure of the ligand TP1 was extracted from the complex co-crystallized identified with the code PDB 3IX3. The geometries of ligands were optimized using the PM3 semiempirical method.  Results:  Two pharmacophoric models were designed, the first one was made using the most active compound (TP-1), highlighting the most important chemical characteristics for molecular recognition. The second model was based on the alignment of three of the most active ligands (TP-1, TP-3 and TP-4). These models were used as a filter in a screening on a database of conformations of several compounds with possible agonist activity of the main circuit of QS present in Pseudomonas aeruginosa. The pharmacophoric model based on alignment of the most active compounds showed greater capacity to select or identify compounds exhibiting significant structural and chemical characteristics to be considered possible hit. With this model, 22 compounds were identified. These compounds were subjected to a series of calculations of docking. The outcomes of the docking were used to identify interactions making a SAR analysis and were used as support to understand how chemically distinct compounds can be accommodated by a highly selective receptor, and provide the framework for the development of novel quorum-sensing regulators, utilizing the 2-benzamido(methyl) phenyl benzoate scaffold and to assess the possibility of synthetic routes, considering the structural similarity presenting between these compounds, generating in this way an alternative to find new compounds with modulating activity QS. These two strategies were used to select a list of potential modulators of quorum sensing or new pharmacophoric candidates.  Conclusions: The two pharmacophoric models designed in this study, the number 2 (model based on the alignment of the most active compounds) showed greater hability to select or identify compounds that had important structural and chemical characteristics to be considered possible hits. With this model, 22 compounds were identified, which were subsequently subjected to docking calculations. In general, the docking protocol used is adequate, since in validating the conformation of the co-crystallized ligand.]]></p></abstract>
<abstract abstract-type="short" xml:lang="es"><p><![CDATA[RESUMEN  Antecedentes: Quorum sensing (QS) es un mecanismo dependiente de la densidad celular que le permite a las bacterias regular la expresión de genes específicos en respuesta a cambios en su densidad poblacional, controlando de esta manera sus actividades, con el fin de producir una respuesta como una unidad multicelular. Estas repuestas incluyen, producción de factores de virulencia, formación de biopelículas, bioluminiscencia, esporulación, entre otros comportamientos.  Objetivos:  Obtener modelos farmacofóricos capaces de filtrar e identificar moléculas con posible actividad agonista del QS y buscar posibles candidatos basados en cálculos de docking molecular.  Métodos:  La estructura del receptor LasR fue obtenida del Protein Data Bank (PDB). El programa utilizando para el acoplamiento fue AutoDock 4.2. Las estructuras de los cuatro compuestos identificados como líderes en el estudio realizado por Muh et al, (2006), fueron utilizadas con el fin de diseñar modelos farmacofóricos capaces de identificar molécu-las con posible actividad agonista del QS. La estructura 3D del ligando TP-1 fue extraída del complejo co-cristalizado identificado con el código PDB 3IX3. Las geometrías de los ligandos obtenidos como resultado de la búsqueda farmacofórica fueron optimizadas usando el método semiempírico PM3, para posteriormente realizar los cálculos de docking molecular.  Resultados:  Se diseñaron dos modelos farmacofóricos, el primero se creó utilizando el compuesto más activo identificado como TP-1, resaltando las características químicas más importantes para el reconocimiento molecular. El segundo modelo se basó en el alineamiento de tres de los ligandos más activos (TP-1, TP-3 y TP-4). Estos modelos se utilizaron como filtro en un cribado sobre una base de datos de conformaciones de varios compuestos con posible actividad agonista del circuito principal de QS presente en Pseudomonas aeruginosa. El modelo farmacofórico basado en el alineamiento de los compuestos más activos se utilizó para seleccionar o identificar los compuestos que presentaban características estructurales y químicas importantes para ser considerados posibles hits. Con este modelo se identificaron 22 compuestos. A estos 22 compuestos se les realizo una serie de cálculos de docking molecular. Los resultados del docking sirvieron para identificar las interacciones haciendo un análisis SAR (structure-activity relationship) y fueron usados como soporte para entender como compuestos distintos químicamente se pueden acoplar selectivamente al receptor LasR y apoyo para evaluar la posibilidad de rutas de síntesis, teniendo en cuenta la similitud estructural que presentan estos compuestos con el núcleo base 2-(benzamidometil) fenil benzoato, generando una alternativa para encontrar nuevos compuestos con actividad agonista del QS. Estas dos estrategias fueron usadas para seleccionar una lista de posibles moduldores del QS e identificar un nuevo farmacofóro.  Conclusiones: Los dos modelos farmacofóricos diseñados en este estudio, el número 2 (modelo basado en la alineación de los compuestos más activos) mostró mayor habilidad para seleccionar o identificar compuestos que tenían las características estructurales y químicas importantes para ser considerados como posibles fármacos. Con este modelo, se identificaron 22 compuestos, los cuales fueron posteriormente sometidos a cálculos de acoplamiento. En general, el protocolo de acoplamiento utilizado fue el adecuado, ya que se validó la conformación del ligando co-cristalizado]]></p></abstract>
<kwd-group>
<kwd lng="en"><![CDATA[Quorum sensing]]></kwd>
<kwd lng="en"><![CDATA[virtual screening]]></kwd>
<kwd lng="en"><![CDATA[Pseudomonas aeruginosa]]></kwd>
<kwd lng="en"><![CDATA[Docking]]></kwd>
<kwd lng="es"><![CDATA[Quorum sensing]]></kwd>
<kwd lng="es"><![CDATA[cribado virtual]]></kwd>
<kwd lng="es"><![CDATA[Pseudomonas aeruginosa]]></kwd>
<kwd lng="es"><![CDATA[acople molecular]]></kwd>
</kwd-group>
</article-meta>
</front><back>
<ref-list>
<ref id="B1">
<label>1</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Miller]]></surname>
<given-names><![CDATA[MB]]></given-names>
</name>
<name>
<surname><![CDATA[Bassler]]></surname>
<given-names><![CDATA[BL]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Ensing in]]></article-title>
<source><![CDATA[Annu Rev Microbiol]]></source>
<year>2001</year>
<volume>55</volume>
<page-range>165-99</page-range></nlm-citation>
</ref>
<ref id="B2">
<label>2</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Galloway]]></surname>
<given-names><![CDATA[WRJD]]></given-names>
</name>
<name>
<surname><![CDATA[Hodgkinson]]></surname>
<given-names><![CDATA[JT]]></given-names>
</name>
<name>
<surname><![CDATA[Bowden]]></surname>
<given-names><![CDATA[S]]></given-names>
</name>
<name>
<surname><![CDATA[Welch]]></surname>
<given-names><![CDATA[M]]></given-names>
</name>
<name>
<surname><![CDATA[Spring]]></surname>
<given-names><![CDATA[DR]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Applications of small molecule activators and inhibitors of quorum sensing in Gram-negative bacteria]]></article-title>
<source><![CDATA[Trends Microbiol]]></source>
<year>2012</year>
<volume>20</volume>
<numero>9</numero>
<issue>9</issue>
<page-range>449-58</page-range></nlm-citation>
</ref>
<ref id="B3">
<label>3</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Higgins]]></surname>
<given-names><![CDATA[DA]]></given-names>
</name>
<name>
<surname><![CDATA[Pomianek]]></surname>
<given-names><![CDATA[ME]]></given-names>
</name>
<name>
<surname><![CDATA[Kraml]]></surname>
<given-names><![CDATA[CM]]></given-names>
</name>
<name>
<surname><![CDATA[Taylor]]></surname>
<given-names><![CDATA[RK]]></given-names>
</name>
<name>
<surname><![CDATA[Semmelhack]]></surname>
<given-names><![CDATA[MF]]></given-names>
</name>
<name>
<surname><![CDATA[Bassler]]></surname>
<given-names><![CDATA[BL]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[The major Vibrio cholerae autoinducer and its role in virulence factor production]]></article-title>
<source><![CDATA[Nature]]></source>
<year>2007</year>
<volume>450</volume>
<numero>7171</numero>
<issue>7171</issue>
<page-range>883-6</page-range></nlm-citation>
</ref>
<ref id="B4">
<label>4</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Marketon]]></surname>
<given-names><![CDATA[MM]]></given-names>
</name>
<name>
<surname><![CDATA[Gronquist]]></surname>
<given-names><![CDATA[MR]]></given-names>
</name>
<name>
<surname><![CDATA[Eberhard]]></surname>
<given-names><![CDATA[A]]></given-names>
</name>
<name>
<surname><![CDATA[González]]></surname>
<given-names><![CDATA[JE]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Characterization of the Sinorhizobium meliloti sinR/sinI locus and the production of novel N-acyl homoserine lactones]]></article-title>
<source><![CDATA[J Bacteriol]]></source>
<year>2002</year>
<volume>184</volume>
<numero>20</numero>
<issue>20</issue>
<page-range>5686-95</page-range></nlm-citation>
</ref>
<ref id="B5">
<label>5</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Kleerebezem]]></surname>
<given-names><![CDATA[M]]></given-names>
</name>
<name>
<surname><![CDATA[Beerthuyzen]]></surname>
<given-names><![CDATA[MM]]></given-names>
</name>
<name>
<surname><![CDATA[Vaughan]]></surname>
<given-names><![CDATA[EE]]></given-names>
</name>
<name>
<surname><![CDATA[De Vos]]></surname>
<given-names><![CDATA[WM]]></given-names>
</name>
<name>
<surname><![CDATA[Kuipers]]></surname>
<given-names><![CDATA[OP]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Controlled gene expression systems for lactic acid bacteria: Transferable nisin-inducible expression cassettes for Lactococcus, Leuconostoc, and Lactobacillus spp]]></article-title>
<source><![CDATA[Appl Environ Microbiol]]></source>
<year>1997</year>
<volume>63</volume>
<numero>11</numero>
<issue>11</issue>
<page-range>4581-4</page-range></nlm-citation>
</ref>
<ref id="B6">
<label>6</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Beck Von]]></surname>
<given-names><![CDATA[S]]></given-names>
</name>
<name>
<surname><![CDATA[Farrand]]></surname>
<given-names><![CDATA[S]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Capsular Polysaccharide Biosynthesis and Pathogenicity in]]></article-title>
<source><![CDATA[Microbiology]]></source>
<year>1995</year>
<volume>177</volume>
<numero>17</numero>
<issue>17</issue>
<page-range>5000-8</page-range></nlm-citation>
</ref>
<ref id="B7">
<label>7</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[González]]></surname>
<given-names><![CDATA[JE]]></given-names>
</name>
<name>
<surname><![CDATA[Marketon]]></surname>
<given-names><![CDATA[MM]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Quorum sensing in nitrogen-fixing rhizobia]]></article-title>
<source><![CDATA[Microbiol Mol Biol Rev]]></source>
<year>2003</year>
<volume>67</volume>
<numero>4</numero>
<issue>4</issue>
<page-range>574-92</page-range></nlm-citation>
</ref>
<ref id="B8">
<label>8</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Henke]]></surname>
<given-names><![CDATA[JM]]></given-names>
</name>
<name>
<surname><![CDATA[Bassler]]></surname>
<given-names><![CDATA[BL]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Bacterial social engagements]]></article-title>
<source><![CDATA[Trends Cell Biol]]></source>
<year>2004</year>
<volume>4</volume>
<numero>11</numero>
<issue>11</issue>
<page-range>648-56</page-range></nlm-citation>
</ref>
<ref id="B9">
<label>9</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Bainton]]></surname>
<given-names><![CDATA[NJ]]></given-names>
</name>
<name>
<surname><![CDATA[Bycroft]]></surname>
<given-names><![CDATA[BW]]></given-names>
</name>
<name>
<surname><![CDATA[Chhabra]]></surname>
<given-names><![CDATA[SR]]></given-names>
</name>
<name>
<surname><![CDATA[Stead]]></surname>
<given-names><![CDATA[P]]></given-names>
</name>
<name>
<surname><![CDATA[Gledhill]]></surname>
<given-names><![CDATA[L]]></given-names>
</name>
<name>
<surname><![CDATA[Hill]]></surname>
<given-names><![CDATA[PJ]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[A general role for the lux autoinducer in bacterial cell signalling: control of antibiotic biosynthesis in Erwinia]]></article-title>
<source><![CDATA[Gene]]></source>
<year>1992</year>
<volume>116</volume>
<numero>1</numero>
<issue>1</issue>
<page-range>87-91</page-range></nlm-citation>
</ref>
<ref id="B10">
<label>10</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Costerton]]></surname>
<given-names><![CDATA[JW]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Cystic fibrosis pathogenesis and the role of bio-films in persistent infection]]></article-title>
<source><![CDATA[Trends Microbiol]]></source>
<year>2001</year>
<volume>9</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>50-2</page-range></nlm-citation>
</ref>
<ref id="B11">
<label>11</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Lyczak]]></surname>
<given-names><![CDATA[JB]]></given-names>
</name>
<name>
<surname><![CDATA[Cannon]]></surname>
<given-names><![CDATA[CL]]></given-names>
</name>
<name>
<surname><![CDATA[Pier]]></surname>
<given-names><![CDATA[GB]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Establishment of Pseudomona aeruginosa infection: Lessons from a versatile opportunist]]></article-title>
<source><![CDATA[Microbes Infect]]></source>
<year>2000</year>
<volume>2</volume>
<numero>9</numero>
<issue>9</issue>
<page-range>1051-60</page-range></nlm-citation>
</ref>
<ref id="B12">
<label>12</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Van Delden]]></surname>
<given-names><![CDATA[C]]></given-names>
</name>
<name>
<surname><![CDATA[Iglewski]]></surname>
<given-names><![CDATA[BH]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Cell-to-cell signaling and Pseudo-mona aeruginosa infections]]></article-title>
<source><![CDATA[Emerg Infect Dis]]></source>
<year>1998</year>
<volume>4</volume>
<numero>4</numero>
<issue>4</issue>
<page-range>551-60</page-range></nlm-citation>
</ref>
<ref id="B13">
<label>13</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Moore]]></surname>
<given-names><![CDATA[JD]]></given-names>
</name>
<name>
<surname><![CDATA[Rossi]]></surname>
<given-names><![CDATA[FM]]></given-names>
</name>
<name>
<surname><![CDATA[Welsh]]></surname>
<given-names><![CDATA[MA]]></given-names>
</name>
<name>
<surname><![CDATA[Nyffeler]]></surname>
<given-names><![CDATA[KE]]></given-names>
</name>
<name>
<surname><![CDATA[Blackwell]]></surname>
<given-names><![CDATA[HE]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[A Comparative Analysis of Synthetic Quorum Sensing Modulators in Pseudomona aeruginosa: New Insights into Mechanism, Active Efflux Susceptibility, Phenotypic Response, and Next-Gene ration Ligand Design]]></article-title>
<source><![CDATA[J Am Chem Soc]]></source>
<year>2015</year>
<volume>137</volume>
<numero>46</numero>
<issue>46</issue>
<page-range>14626-39</page-range></nlm-citation>
</ref>
<ref id="B14">
<label>14</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Müh]]></surname>
<given-names><![CDATA[U]]></given-names>
</name>
<name>
<surname><![CDATA[Schuster]]></surname>
<given-names><![CDATA[M]]></given-names>
</name>
<name>
<surname><![CDATA[Heim]]></surname>
<given-names><![CDATA[R]]></given-names>
</name>
<name>
<surname><![CDATA[Singh]]></surname>
<given-names><![CDATA[A]]></given-names>
</name>
<name>
<surname><![CDATA[Olson]]></surname>
<given-names><![CDATA[ER]]></given-names>
</name>
<name>
<surname><![CDATA[Greenberg]]></surname>
<given-names><![CDATA[EP]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Novel Pseudomona aeruginosa quorum-sensing inhibitors identified in an ultra-high-throughput screen]]></article-title>
<source><![CDATA[Antimicrob Agents Chemother]]></source>
<year>2006</year>
<volume>50</volume>
<numero>11</numero>
<issue>11</issue>
<page-range>3674-9</page-range></nlm-citation>
</ref>
<ref id="B15">
<label>15</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Smith]]></surname>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Library Screening for Synthetic Agonists and Antagonists of a Pseudomona aeruginosa Autoinducer]]></article-title>
<source><![CDATA[Acta Biochim Pol]]></source>
<year>2005</year>
<volume>52</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>507-13</page-range></nlm-citation>
</ref>
<ref id="B16">
<label>16</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Srinivas Reddy]]></surname>
<given-names><![CDATA[A.]]></given-names>
</name>
<name>
<surname><![CDATA[Priyadarshini Pati,]]></surname>
<given-names><![CDATA[S.]]></given-names>
</name>
<name>
<surname><![CDATA[Praveen Kumar]]></surname>
<given-names><![CDATA[P.]]></given-names>
</name>
<name>
<surname><![CDATA[Pradeep]]></surname>
<given-names><![CDATA[HN]]></given-names>
</name>
<name>
<surname><![CDATA[Sastry]]></surname>
<given-names><![CDATA[GN.]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Virtual Screening in Drug Discovery - A Computational Perspective]]></article-title>
<source><![CDATA[Current protein &amp; peptide science]]></source>
<year>2007</year>
<volume>8</volume>
<page-range>329-51</page-range></nlm-citation>
</ref>
<ref id="B17">
<label>17</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Scior]]></surname>
<given-names><![CDATA[T]]></given-names>
</name>
<name>
<surname><![CDATA[Bender]]></surname>
<given-names><![CDATA[A]]></given-names>
</name>
<name>
<surname><![CDATA[Tresadern]]></surname>
<given-names><![CDATA[G]]></given-names>
</name>
<name>
<surname><![CDATA[Medina-Franco]]></surname>
<given-names><![CDATA[JL]]></given-names>
</name>
<name>
<surname><![CDATA[Martínez-Mayorga]]></surname>
<given-names><![CDATA[K]]></given-names>
</name>
<name>
<surname><![CDATA[Langer]]></surname>
<given-names><![CDATA[T]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Recognizing pitfalls in virtual screening: A critical review]]></article-title>
<source><![CDATA[J Chem Inf Model]]></source>
<year>2012</year>
<volume>52</volume>
<numero>4</numero>
<issue>4</issue>
<page-range>867-81</page-range></nlm-citation>
</ref>
<ref id="B18">
<label>18</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Huang]]></surname>
<given-names><![CDATA[SY]]></given-names>
</name>
<name>
<surname><![CDATA[Zou]]></surname>
<given-names><![CDATA[X]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Advances and challenges in Protein-ligand docking]]></article-title>
<source><![CDATA[Int J Mol Sci]]></source>
<year>2010</year>
<volume>11</volume>
<numero>8</numero>
<issue>8</issue>
<page-range>3016-34</page-range></nlm-citation>
</ref>
<ref id="B19">
<label>19</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Zou]]></surname>
<given-names><![CDATA[Y]]></given-names>
</name>
<name>
<surname><![CDATA[Nair]]></surname>
<given-names><![CDATA[SK]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Molecular Basis for the Recognition of Structurally Distinct Autoinducer Mimics by the Pseudomona aeruginosa LasR Quorum-Sensing Signaling Receptor]]></article-title>
<source><![CDATA[Chem Biol]]></source>
<year>2009</year>
<volume>16</volume>
<numero>9</numero>
<issue>9</issue>
<page-range>961-70</page-range></nlm-citation>
</ref>
<ref id="B20">
<label>20</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Bolton]]></surname>
<given-names><![CDATA[EE]]></given-names>
</name>
<name>
<surname><![CDATA[Wang]]></surname>
<given-names><![CDATA[Y]]></given-names>
</name>
<name>
<surname><![CDATA[Thiessen]]></surname>
<given-names><![CDATA[PA]]></given-names>
</name>
<name>
<surname><![CDATA[Bryant]]></surname>
<given-names><![CDATA[SH]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[PubChem: Inte-grated Platform of Small Molecules and Biological Activities]]></article-title>
<source><![CDATA[Annual Reports in Computational Chemistry]]></source>
<year>2008</year>
<volume>4</volume>
<page-range>217-41</page-range><publisher-name><![CDATA[Elsevier B.V]]></publisher-name>
</nlm-citation>
</ref>
<ref id="B21">
<label>21</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Müh]]></surname>
<given-names><![CDATA[U]]></given-names>
</name>
<name>
<surname><![CDATA[Hare]]></surname>
<given-names><![CDATA[BJ]]></given-names>
</name>
<name>
<surname><![CDATA[Duerkop]]></surname>
<given-names><![CDATA[B a]]></given-names>
</name>
<name>
<surname><![CDATA[Schuster]]></surname>
<given-names><![CDATA[M]]></given-names>
</name>
<name>
<surname><![CDATA[Hanzelka]]></surname>
<given-names><![CDATA[BL]]></given-names>
</name>
<name>
<surname><![CDATA[Heim]]></surname>
<given-names><![CDATA[R]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[A structurally unrelated mimic of a Pseudomona aeruginosa acyl-homoserine lactone quorum-sensing signal]]></article-title>
<source><![CDATA[Proc Natl Acad Sci U S A]]></source>
<year>2006</year>
<volume>103</volume>
<page-range>16948-52</page-range></nlm-citation>
</ref>
<ref id="B22">
<label>22</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Geske]]></surname>
<given-names><![CDATA[GD]]></given-names>
</name>
<name>
<surname><![CDATA[O&#8217;Neill]]></surname>
<given-names><![CDATA[JC]]></given-names>
</name>
<name>
<surname><![CDATA[Miller]]></surname>
<given-names><![CDATA[DM]]></given-names>
</name>
<name>
<surname><![CDATA[Mattmann]]></surname>
<given-names><![CDATA[ME]]></given-names>
</name>
<name>
<surname><![CDATA[Blackwell]]></surname>
<given-names><![CDATA[HE]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[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]]></article-title>
<source><![CDATA[J Am Chem Soc]]></source>
<year>2007</year>
<volume>129</volume>
<numero>44</numero>
<issue>44</issue>
<page-range>13613-25</page-range></nlm-citation>
</ref>
<ref id="B23">
<label>23</label><nlm-citation citation-type="">
<collab>Chemical Computing Group</collab>
<source><![CDATA[MOE. (Molecular Operating Environment)]]></source>
<year>2009</year>
<volume>2009.10 Re</volume>
<page-range>32</page-range></nlm-citation>
</ref>
<ref id="B24">
<label>24</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Vyas]]></surname>
<given-names><![CDATA[V]]></given-names>
</name>
<name>
<surname><![CDATA[Jain]]></surname>
<given-names><![CDATA[A]]></given-names>
</name>
<name>
<surname><![CDATA[Jain]]></surname>
<given-names><![CDATA[A]]></given-names>
</name>
<name>
<surname><![CDATA[Gupta]]></surname>
<given-names><![CDATA[A]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Virtual screening: A fast tool for drug design]]></article-title>
<source><![CDATA[Sci Pharm]]></source>
<year>2008</year>
<volume>76</volume>
<numero>3</numero>
<issue>3</issue>
<page-range>333-60</page-range></nlm-citation>
</ref>
<ref id="B25">
<label>25</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Përez-Nueno]]></surname>
<given-names><![CDATA[VI]]></given-names>
</name>
<name>
<surname><![CDATA[Ritchie]]></surname>
<given-names><![CDATA[DW]]></given-names>
</name>
<name>
<surname><![CDATA[Rabal]]></surname>
<given-names><![CDATA[O]]></given-names>
</name>
<name>
<surname><![CDATA[Pascual]]></surname>
<given-names><![CDATA[R]]></given-names>
</name>
<name>
<surname><![CDATA[Borrella]]></surname>
<given-names><![CDATA[JI]]></given-names>
</name>
<name>
<surname><![CDATA[Teixidó]]></surname>
<given-names><![CDATA[J]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Comparison of ligand-based and receptor-based virtual screening of HIV entry inhibitors for the CXCR4 and CCR5 receptors using 3D ligand shape matching and ligand-receptor docking]]></article-title>
<source><![CDATA[J Chem Inf Model]]></source>
<year>2008</year>
<volume>48</volume>
<numero>3</numero>
<issue>3</issue>
<page-range>509-33</page-range></nlm-citation>
</ref>
<ref id="B26">
<label>26</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Bernstein]]></surname>
<given-names><![CDATA[FC]]></given-names>
</name>
<name>
<surname><![CDATA[Koetzle]]></surname>
<given-names><![CDATA[TF]]></given-names>
</name>
<name>
<surname><![CDATA[Williams]]></surname>
<given-names><![CDATA[GJB]]></given-names>
</name>
<name>
<surname><![CDATA[Meyer]]></surname>
<given-names><![CDATA[EF]]></given-names>
</name>
<name>
<surname><![CDATA[Brice]]></surname>
<given-names><![CDATA[MD]]></given-names>
</name>
<name>
<surname><![CDATA[Rodgers]]></surname>
<given-names><![CDATA[JR]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[The protein data bank: A computer-based archival file for macromolecular structures]]></article-title>
<source><![CDATA[Arch Biochem Biophys]]></source>
<year>1978</year>
<volume>185</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>584-91</page-range></nlm-citation>
</ref>
<ref id="B27">
<label>27</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Morris]]></surname>
<given-names><![CDATA[G]]></given-names>
</name>
<name>
<surname><![CDATA[Huey]]></surname>
<given-names><![CDATA[R]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility]]></article-title>
<source><![CDATA[J Comput Chem]]></source>
<year>2009</year>
<volume>30</volume>
<numero>16</numero>
<issue>16</issue>
<page-range>2785-91</page-range></nlm-citation>
</ref>
<ref id="B28">
<label>28</label><nlm-citation citation-type="">
<collab>Tripos International</collab>
<source><![CDATA[Sybyl, version 7.3; software for molecular modeling package]]></source>
<year>2007</year>
</nlm-citation>
</ref>
<ref id="B29">
<label>29</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Stewart]]></surname>
<given-names><![CDATA[JJP]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Optimization of Parameters for Semiempiri-cal Methods .2. Applications]]></article-title>
<source><![CDATA[J Comput Chem]]></source>
<year>1989</year>
<volume>10</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>221-64</page-range></nlm-citation>
</ref>
<ref id="B30">
<label>30</label><nlm-citation citation-type="">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Frisch]]></surname>
<given-names><![CDATA[M. J.]]></given-names>
</name>
<name>
<surname><![CDATA[Trucks]]></surname>
<given-names><![CDATA[G. W.]]></given-names>
</name>
<name>
<surname><![CDATA[Schlegel]]></surname>
<given-names><![CDATA[H. B.]]></given-names>
</name>
<name>
<surname><![CDATA[Scuseria]]></surname>
<given-names><![CDATA[G. E.]]></given-names>
</name>
<name>
<surname><![CDATA[Robb]]></surname>
<given-names><![CDATA[M. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Cheeseman]]></surname>
<given-names><![CDATA[J. R.]]></given-names>
</name>
<name>
<surname><![CDATA[Montgomery]]></surname>
<given-names><![CDATA[J. A.]]></given-names>
</name>
<name>
<surname><![CDATA[Vreven]]></surname>
<given-names><![CDATA[T.]]></given-names>
</name>
<name>
<surname><![CDATA[Kudin]]></surname>
<given-names><![CDATA[K. N.]]></given-names>
</name>
<name>
<surname><![CDATA[Burant]]></surname>
<given-names><![CDATA[J. C.]]></given-names>
</name>
<name>
<surname><![CDATA[Millam]]></surname>
<given-names><![CDATA[J. M.]]></given-names>
</name>
<name>
<surname><![CDATA[Iyengar]]></surname>
<given-names><![CDATA[S. S.]]></given-names>
</name>
<name>
<surname><![CDATA[Tomasi]]></surname>
<given-names><![CDATA[J.]]></given-names>
</name>
<name>
<surname><![CDATA[Barone]]></surname>
<given-names><![CDATA[V.]]></given-names>
</name>
<name>
<surname><![CDATA[Mennucci]]></surname>
<given-names><![CDATA[B.]]></given-names>
</name>
<name>
<surname><![CDATA[Cossi]]></surname>
<given-names><![CDATA[M.]]></given-names>
</name>
<name>
<surname><![CDATA[Scalmani]]></surname>
<given-names><![CDATA[G.]]></given-names>
</name>
<name>
<surname><![CDATA[Rega]]></surname>
<given-names><![CDATA[N]]></given-names>
</name>
</person-group>
<source><![CDATA[G.A.P.G. Gaussian03. 3AD]]></source>
<year></year>
</nlm-citation>
</ref>
<ref id="B31">
<label>31</label><nlm-citation citation-type="">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Sanner]]></surname>
<given-names><![CDATA[F. M. Python]]></given-names>
</name>
</person-group>
<source><![CDATA[A Programming Language for Software Integration and Development]]></source>
<year>1999</year>
<page-range>57-61</page-range></nlm-citation>
</ref>
<ref id="B32">
<label>32</label><nlm-citation citation-type="">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Gasteiger]]></surname>
<given-names><![CDATA[J]]></given-names>
</name>
<name>
<surname><![CDATA[Marsili]]></surname>
<given-names><![CDATA[M]]></given-names>
</name>
</person-group>
<source><![CDATA[Tetrahedron]]></source>
<year>1980</year>
<page-range>3219-88</page-range></nlm-citation>
</ref>
<ref id="B33">
<label>33</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Morris]]></surname>
<given-names><![CDATA[GM]]></given-names>
</name>
<name>
<surname><![CDATA[Goodsell]]></surname>
<given-names><![CDATA[DS]]></given-names>
</name>
<name>
<surname><![CDATA[Halliday]]></surname>
<given-names><![CDATA[RS]]></given-names>
</name>
<name>
<surname><![CDATA[Huey]]></surname>
<given-names><![CDATA[R]]></given-names>
</name>
<name>
<surname><![CDATA[Hart]]></surname>
<given-names><![CDATA[WE]]></given-names>
</name>
<name>
<surname><![CDATA[Belew]]></surname>
<given-names><![CDATA[RK]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function]]></article-title>
<source><![CDATA[J Comput Chem]]></source>
<year>1998</year>
<volume>19</volume>
<numero>14</numero>
<issue>14</issue>
<page-range>1639-62</page-range></nlm-citation>
</ref>
<ref id="B34">
<label>34</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ahumedo]]></surname>
<given-names><![CDATA[M]]></given-names>
</name>
<name>
<surname><![CDATA[Díaz]]></surname>
<given-names><![CDATA[A]]></given-names>
</name>
<name>
<surname><![CDATA[Vivas-Reyes]]></surname>
<given-names><![CDATA[R]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[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 antiquorum sensing activity]]></article-title>
<source><![CDATA[Eur J Med Chem]]></source>
<year>2010</year>
<volume>45</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>608-15</page-range></nlm-citation>
</ref>
<ref id="B35">
<label>35</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Ahumedo]]></surname>
<given-names><![CDATA[M]]></given-names>
</name>
<name>
<surname><![CDATA[Drosos]]></surname>
<given-names><![CDATA[JC]]></given-names>
</name>
<name>
<surname><![CDATA[Vivas-Reyes]]></surname>
<given-names><![CDATA[R]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[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]]></article-title>
<source><![CDATA[Mol Biosyst]]></source>
<year>2014</year>
<volume>10</volume>
<numero>5</numero>
<issue>5</issue>
<page-range>1162-71</page-range></nlm-citation>
</ref>
<ref id="B36">
<label>36</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Soulère]]></surname>
<given-names><![CDATA[L]]></given-names>
</name>
<name>
<surname><![CDATA[Frezza]]></surname>
<given-names><![CDATA[M]]></given-names>
</name>
<name>
<surname><![CDATA[Queneau]]></surname>
<given-names><![CDATA[Y]]></given-names>
</name>
<name>
<surname><![CDATA[Doutheau]]></surname>
<given-names><![CDATA[A]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[Exploring the active site of acyl homoserine lactones-dependent transcriptional regulators with bacterial quorum sensing modulators using molecular mechanics and docking studies]]></article-title>
<source><![CDATA[J Mol Graph Model]]></source>
<year>2007</year>
<volume>26</volume>
<numero>2</numero>
<issue>2</issue>
<page-range>581-90</page-range></nlm-citation>
</ref>
<ref id="B37">
<label>37</label><nlm-citation citation-type="journal">
<person-group person-group-type="author">
<name>
<surname><![CDATA[Warren]]></surname>
<given-names><![CDATA[GL]]></given-names>
</name>
<name>
<surname><![CDATA[Andrews C]]></surname>
<given-names><![CDATA[V]]></given-names>
</name>
<name>
<surname><![CDATA[Capelli]]></surname>
<given-names><![CDATA[A]]></given-names>
</name>
<name>
<surname><![CDATA[Clarke]]></surname>
<given-names><![CDATA[B]]></given-names>
</name>
<name>
<surname><![CDATA[LaLonde]]></surname>
<given-names><![CDATA[J]]></given-names>
</name>
<name>
<surname><![CDATA[Lambert]]></surname>
<given-names><![CDATA[MH]]></given-names>
</name>
</person-group>
<article-title xml:lang=""><![CDATA[A critical assessment of docking programs and scoring functions]]></article-title>
<source><![CDATA[J Med Chem]]></source>
<year>2006</year>
<volume>49</volume>
<numero>20</numero>
<issue>20</issue>
<page-range>5912-31</page-range></nlm-citation>
</ref>
</ref-list>
</back>
</article>
