This is a continuation application for a program aimed at development of new drugs for the treatment of human acquired immunodeficiency syndrome by interference with HIV-1 RNA transcription. Our studies have focused on the pyrrole-imidazole polyamides, developed in the laboratory of the Co-PI, Dr. Peter Dervan at Caltech. These molecules can be designed and synthesized to target a wide range of DNA sequences with subnanomolar affinities, comparable to the affinities of cellular transcription factors for their DNA targets. During the previous years of support, we have developed polyamide ligands to target the binding sites for the host cell regulatory proteins involved in HIV-l RNA transcription. Studies in the laboratory of Dr. J. Gottesfeld at the Scripps Research Institute have shown that these molecules inhibit specific transcription factor-DNA interactions on the HIV-1 promoter and enhancer and are potent inhibitors of HIV-1 transcription in vitro. Importantly, through a collaborative effort with Dr. D. Mosier at Scripps, we have shown that these polyamides are effective inhibitors of HIV-1 replication in human peripheral blood lymphocytes. We now propose to optimize our DNA targets within the HIV-1 enhancer and promoter elements and to validate the hypothesis that inhibition of virus replication is a direct consequence of inhibition of protein-DNA interactions on the integrated HIV-1 proviral DNA. We will determine whether polyamides can access their target sequences in the context of cellular chromatin and we will examine the genome-wide effects of polyamide treatment using DNA array technology. Given our success in inhibition of virus replication in cell culture, we propose collaborative preclinical studies with the Mosier laboratory to determine the effectiveness of polyamides in the human PBL-SCID mouse model.
