Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR

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 lig ands to bind to a TAR RNA structure using a four-step docking procedure: ri gid docking first, followed by three steps of flexible docking using a pseu dobrownian Monte Carlo minimization in torsion angle space with progressive ly more detailed conformational sampling on a progressively smaller list of top-ranking compounds. To validate the procedure, we successfully docked l igands for five RNA complexes of known structure. For ranking ligands accor ding to binding avidity, an empirical binding free energy function was deve loped which accounts, in particular, for solvation, isomerization free ener gy, and changes in conformational entropy. System-specific parameters for t he function were derived on a training set of RNA/ligand complexes with kno wn structure and affinity. To validate the free energy function, we screene d the entire ACD for ligands for an RNA aptamer which binds L-arginine tigh tly. The native ligand ranked 17 out of ca. 153,000 compounds screened, i.e ., the procedure is able to filter out > 99.98% of the database and still r etain the native ligand. Screening of the ACD for TAR ligands yielded a hig h rank for all known TAR ligands contained in the ACD and suggested several other potential TAR ligands. Eight of the highest ranking compounds not pr eviously known to be ligands were assayed for inhibition of the Tat-TAR int eraction, and two exhibited a CD50 of ca. 1 mu M.