Harnessing the Power of Small Molecules to Target Nucleic Acids

Nucleic acids provide potentially powerful targets for many disease-related processes, particularly those where protein targeting has been untenable. Pyrrole-imidazole polyamides are programmable small molecules that bind strongly and sequence-specifically to the minor groove of DNA and offer the opportunity to target the transcription factor - DNA interface. Recent work in prostate cancer has identified Py-Im polyamides that abrogate the AR-driven transcription of the ERG oncoprotein, inhibit ERG-driven changes in gene expression, and decrease levels of ERG-dependent DNA damage. Conversely, as the varied and important roles of RNA become increasingly appreciated in both fundamental biology and disease, the lack of effective targeting strategies for RNA becomes increasingly apparent. In line with our long term goals of elucidating novel RNA structures and functions, we are currently involved in the development of an RNA-targeted small molecule library as well as improved strategies for screening through small molecule microarrays and multivalent ligand assembly. Initial efforts have focused on identifying probes for HIV-1 trans activation responsive element (TAR) RNA in collaboration with the Al-Hashimi group in Duke Biochemistry. With the assistance of computational docking, we have designed a series of amiloride derivatives based on the previously reported apical loop binder dimethyl amiloride (DMA). We have developed general synthetic routes for rapid, parallel synthesis and have evaluated the activity of select derivatives in fluorescent TAR-Tat displacement as well as NMR based assays. These initial efforts have yielded ligands with two to ten-fold improved activity relative to DMA. Several applications and future directions will also be discussed, particularly our interest in the detection, characterization, and inhibition of long noncoding RNAs in prostate cancer.

Amanda E. Hargrove became an Assistant Professor of Chemistry at Duke University in August, 2013. Previous training included an NIH postdoctoral fellowship with Professor Peter B. Dervan at the California Institute of Technology where Dr. Hargrove employed DNA-binding pyrrole-imidazole polyamides to alter AR- and ERG-related expression and phenotypes in prostate cancer cells along with the determination of their aggregation propensity and in vivo pharmacokinetic behavior. Dr. Hargrove's doctoral research at the University of Texas at Austin where she was jointly advised by Professors Eric V. Anslyn and Jonathan L. Sessler and collaborated closely with Professor Andrew D. Ellington led to the first published recognition system for steroid-carbohydrate conjugates as well as the use of nucleic acids in self-assembled multi-functional receptors. Drawing on these previous interdisciplinary experiences, the Hargrove lab at Duke is focused on developing small molecule probes to investigate the structure and function of RNA molecules relevant to human disease. Strategies include virtual screening to identify novel chemical space as well as the creation of a diverse small molecule microarray targeted to RNA, which will be used as a platform for the discovery of novel multivalent RNA-binding agents and for the interrogation of RNA secondary structures and associated proteins through pattern recognition.  Our current targets include viral RNA structures, particularly in HIV, and long noncoding RNAs (lncRNAs) important to advanced prostate cancer.