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New inhibitors of the Tat-TAR RNA interaction found with a "fuzzy" pharmacophore model. | LitMetric

New inhibitors of the Tat-TAR RNA interaction found with a "fuzzy" pharmacophore model.

Chembiochem

Beilstein Endowed Chair for Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Johann-Wolfgang-Goethe-Universität, Marie-Curie-Strasse 11, 60439 Frankfurt am Main, Germany.

Published: June 2005

TAR RNA is a potential target for AIDS therapy. Ligand-based virtual screening was performed to retrieve novel scaffolds for RNA-binding molecules capable of inhibiting the Tat-TAR interaction, which is essential for HIV replication. We used a "fuzzy" pharmacophore approach (SQUID) and an alignment-free pharmacophore method (CATS3D) to carry out virtual screening of a vendor database of small molecules and to perform "scaffold-hopping". 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 (IC50 = 46 microM). The hits had molecular scaffolds different from those of the reference molecules.

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http://dx.doi.org/10.1002/cbic.200400376DOI Listing

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