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We used a \u201cfuzzy\u201d pharmacophore approach (SQUID) and an alignment\u2010free pharmacophore method (CATS3D) to carry out virtual screening of a vendor database of small molecules and to perform \u201cscaffold\u2010hopping\u201d. A small subset of 19 candidate molecules were experimentally tested for TAR RNA binding in a fluorescence resonance energy transfer (FRET) assay. Both methods retrieved molecules that exhibited activities comparable to those of the reference molecules acetylpromazine and chlorpromazine, with the best molecule showing ten times better binding behavior (IC<jats:sub>50<\/jats:sub>=46 \u03bc<jats:sc>M<\/jats:sc>). The hits had molecular scaffolds different from those of the reference molecules.<\/jats:italic><\/jats:p>","DOI":"10.1002\/cbic.200400376","type":"journal-article","created":{"date-parts":[[2005,5,10]],"date-time":"2005-05-10T06:18:16Z","timestamp":1115705896000},"page":"1119-1125","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":42,"title":["New Inhibitors of the Tat\u2013TAR RNA Interaction Found with a \u201cFuzzy\u201d Pharmacophore Model"],"prefix":"10.1002","volume":"6","author":[{"given":"Steffen","family":"Renner","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Verena","family":"Ludwig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver","family":"Boden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ute","family":"Scheffer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"G\u00f6bel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gisbert","family":"Schneider","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2005,5,30]]},"reference":[{"key":"e_1_2_7_1_2","unstructured":"Special journal issues on RNA as drug target:"},{"key":"e_1_2_7_2_2","doi-asserted-by":"publisher","DOI":"10.1002\/bip.10490"},{"key":"e_1_2_7_3_2","doi-asserted-by":"publisher","DOI":"10.1002\/cbic.200390111"},{"key":"e_1_2_7_4_2","unstructured":"\u00a0"},{"key":"e_1_2_7_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1359-6446(03)02624-2"},{"key":"e_1_2_7_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0079-6468(08)70069-9"},{"key":"e_1_2_7_7_2","doi-asserted-by":"publisher","DOI":"10.1021\/ar000118k"},{"key":"e_1_2_7_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1367-5931(00)00142-3"},{"key":"e_1_2_7_9_2","doi-asserted-by":"publisher","DOI":"10.1002\/bip.10410"},{"key":"e_1_2_7_10_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1999.3060"},{"key":"e_1_2_7_11_2","unstructured":"\u00a0"},{"key":"e_1_2_7_12_2","doi-asserted-by":"publisher","DOI":"10.1002\/cbic.200300652"},{"key":"e_1_2_7_13_2","doi-asserted-by":"publisher","DOI":"10.2174\/1568026023393200"},{"key":"e_1_2_7_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1074-5521(02)00151-5"},{"key":"e_1_2_7_15_2","doi-asserted-by":"publisher","DOI":"10.1021\/ci0341161"},{"key":"e_1_2_7_16_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja0398870"},{"key":"e_1_2_7_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1074-5521(02)00106-0"},{"key":"e_1_2_7_18_2","unstructured":"\u00a0"},{"key":"e_1_2_7_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1359-6446(01)02091-8"},{"key":"e_1_2_7_20_2","volume-title":"Virtual Screening for Bioactive Molecules","year":"2000"},{"key":"e_1_2_7_21_2","doi-asserted-by":"publisher","DOI":"10.1023\/A:1008121029716"},{"key":"e_1_2_7_22_2","unstructured":"\u00a0"},{"key":"e_1_2_7_23_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi010680y"},{"key":"e_1_2_7_24_2","doi-asserted-by":"publisher","DOI":"10.1038\/79575"},{"key":"e_1_2_7_25_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1521-3757(19991004)111:19<3068::AID-ANGE3068>3.0.CO;2-0"},{"key":"e_1_2_7_25_3","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1521-3773(19991004)38:19<2894::AID-ANIE2894>3.0.CO;2-F"},{"key":"e_1_2_7_26_2","doi-asserted-by":"publisher","DOI":"10.1021\/jm031139y"},{"key":"e_1_2_7_27_2","doi-asserted-by":"publisher","DOI":"10.1023\/B:JCAM.0000017375.61558.ad"},{"key":"e_1_2_7_28_2","doi-asserted-by":"publisher","DOI":"10.1002\/3527603948.ch13"},{"key":"e_1_2_7_29_2","unstructured":"Specs Delftechpark 30 2628 XH Delft The Netherlands;http:\/\/www.specs.net."},{"key":"e_1_2_7_30_2","unstructured":"MOE Molecular Operating Environment version 2004.03 Chemical Computing Group Inc. 1010 Sherbrooke St. West 910 Montreal Canada."},{"key":"e_1_2_7_31_2","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1002\/(SICI)1096-987X(199604)17:5\/6<490::AID-JCC1>3.0.CO;2-P","author":"Halgren T. 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