Studies of binding constants and interaction of drugs to trans-activation response RNA by capillary electrophoresis

The interaction and binding abilities between the trans-activation response (TAR) element, residues 1-59 of the human immunodeficiency virus type 1 (HIV-1) mRNA, and four computer-simulated designed potentially small-molecule drugs were studied by capillary zone electrophoresis (CZE). Experimental results indicated that these computer-simulated small-molecule drugs could specifically bind to TAR RNA and effectively inhibit the complex formation of HIV-1 trans-activator of transcription (Tat) protein to TAR RNA - an essential component for HIV-1 transcription. The small molecular inhibitors and TAR RNA could be baselinely separated for each individual drug under optimized CE experimental conditions. Their binding constants were quantitatively determined and the data were used for the drug evaluation and screen in lead discovery.