This application is aimed at the development of a new class of small molecule therapeutics for human cancer. Synthetic pyrrole-imidizole polyamides have been shown to bind predetermined DNA sequences with subnanomolar affinities, comparable to the binding affinities of natural transcriptional regulatory proteins; moreover, these molecules inhibit transcription factor-DNA interactions and gene expression both in vitro and in cultured cells. A specific polyamide-DNA alkylator (chlorambucil) conjugate has been identified that alters the morphology and growth characteristics of colon carcinoma cells in culture, and causes these cells to arrest in the G2/M stage of the cell cycle, without any apparent cytotoxicity. Cells treated with this compound fail to grow in soft agar, and do not form tumors in nude mice, indicating that polyamide-treated cells are no longer tumorigenic. Importantly, this compound is active in vivo, reversing the proliferating potential of metastatic colon carcinoma cells in immunocompromised mice. Microarray analysis has given us the striking result that only one gene is significantly down regulated by this polyamide, and RT-PCR and western blotting experiments confirm that histone H4 mRNA and protein is indeed down regulated by this polyamide. To follow up on these observations, polyamide-chlorambucil conjugates will be screened for their effects on cancer cell proliferation both in cell culture and in animal models for various human cancers. The genomic targets of polyamides that inhibit cancer cell growth will be assessed using high density DNA microarray/hybridization methodology, and verified by other methods. The mechanism of inhibition of transcription by polyamides will be assessed both in vitro, in cell culture and in animal models.
