Document Type



Doctor of Philosophy


Chemistry, Organic

Date of Defense


Graduate Advisor

James Bashkin, PhD


Eike Bauer, PhD

Bruce Hamper, PhD

Janet Wilking, PhD



Pyrrole-imidazole polyamides (PAs) are small molecules that typically develop H-bonds to bind to the minor groove of DNA. PAs are of interest because they can be designed to recognize DNA sequences. PAs have numerous biomedical applications in areas like regulation of gene expression and antimicrobial activity. Specifically, polyamide UMSL1011 (a polyamide synthesized in Dr. Bashkin's lab) inhibits replicating vesicular stomatitis virus (VSV) by binding the viral RNA inside the nucleocapsid, as indicated by research at Professor Ming Luo's lab at Georgia State University. However, some reports have revealed that polyamides have a low affinity for “simple” double-stranded RNA. Nevertheless, those reports became insignificant after our joint report of the crystal structure of UMSL1011 binding RNA inside a VSV nucleocapsid-like particle, where the polyamide makes strong contacts with both RNA and protein.

Our goal was to synthesize new PA molecules based on the active shape of UMSL1011 in the crystal structure, which is unlike that of any previously characterized polyamide (for example, the rings of UMSL1011 are not π-stacked when bound to the VSV nucleocapsid and genomic RNA, but they are π-stacked in other known structures). We used the information‐rich crystal structure to help design these new PAs and submitted the compounds for additional cell culture testing against VSV, eventually hoping to test the most active compounds against the respiratory syncytial virus, RSV. We chose VSV as an initial experimental virus because VSV does not kill cells as quickly as the clinical target RSV, presenting a better opportunity to measure antiviral candidates' protection.

The first part of this report describes building a molecule that mimics the truncated portion of UMSL1011. The building blocks were linked to β-alanine PAM resin via solid-phase methods. Cleavage of the compound from PAM resin under mild conditions was essential to maintain the compound's stability. The second part of this report focuses on building several short-long polyamide chains with remarkable modification by substituting three N-terminus groups on either pyrrole or imidazole moieties to enforce the binding with genomic RNA.

Available for download on Wednesday, May 04, 2022