Synthesis and Biological Studies of DNA-binding Cyclic Py-Im Polyamides

• Main Author: Li, Benjamin Chun Yeung
• Format: Others
• Published: 2013
• Online Access: https://thesis.library.caltech.edu/7496/1/BenLi%20Thesis%20Final%20Edit.pdf; Li, Benjamin Chun Yeung (2013) Synthesis and Biological Studies of DNA-binding Cyclic Py-Im Polyamides. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/82YX-QB29. https://resolver.caltech.edu/CaltechTHESIS:02282013-171348639 <https://resolver.caltech.edu/CaltechTHESIS:02282013-171348639>

Pyrrole-imidazole (Py-Im) polyamides are programmable oligomers that bind to the minor groove of DNA in a sequence-specific manner at affinities comparable to natural DNA-binding proteins. Hairpin polyamides have been shown to localize within the nucleus of live cells, disrupt protein-DNA interactions, and modulate endogenous gene expression. Cyclic polyamides display further enhanced DNA binding affinities and exhibit similar gene regulatory effects, but investigations into their biological activity have been limited by the lack of effective synthetic methods. Herein, we demonstrate the efficient synthesis of a focused library of cyclic polyamide utilizing a novel microwave-assisted solid-phase technique. The orthogonal protection strategy allowed for selective turn modifications, and the mild cleavage conditions gave access to polyamide cores beginning with a C-terminal imidazole. In addition to expanding our synthetic repertoire, we further examined the cytotoxicity and cell uptake profiles of the cyclic polyamide variants, which highlighted the significant changes in biological activity resulting from minor structural modifications. Molecular recognition of the polyamide turn unit was also explored by installing heteroatom substituents at the α-position. Interestingly, while none of the fluoro, hydroxyl, or amino derivatives increased turn specificity, the (S)-fluoro turn exhibited better tolerance for binding a C•G pair. Finally, we optimized the synthesis of several biologically active hairpin polyamides on a 50-mg scale and examined their antitumor activity in mice xenograft models.