Summary: Journal of Computer-Aided Molecular Design, 14: 593610, 2000.
© 2000 Kluwer Academic Publishers. Printed in the Netherlands.
Identification of ligands for RNA targets via structure-based virtual
screening: HIV-1 TAR
Anton V. Filikova,, Venkatraman Mohanb, Timothy A. Vickersb, Richard H. Griffeyb, P. Dan
Cookb, Ruben A. Abagyanc & Thomas L. Jamesa,
aDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143-0446, U.S.A.; bIsis
Pharmaceuticals, Inc., Carlsbad, CA 92008-7208, U.S.A.; cMolsoft, L.L.C., P.O. Box 113, Metuchen, NJ 08840,
Received 26 May 1999; Accepted 18 February 2000
Key words: binding free energy, molecular docking, RNA structure, scintillation proximity assay, structure-based
Binding of the Tat protein to TAR RNA is necessary for viral replication of HIV-1. We screened the Available
Chemicals Directory (ACD) to identify ligands to bind to a TAR RNA structure using a four-step docking pro-
cedure: rigid docking first, followed by three steps of flexible docking using a pseudobrownian Monte Carlo
minimization in torsion angle space with progressively more detailed conformational sampling on a progressively
smaller list of top-ranking compounds. To validate the procedure, we successfully docked ligands for five RNA