Synthesis and Characterizing a Novel Polyamide to Inhibit Replication of Viral Protein inside RNA Molecule

N-methyl pyrrole/N-methyl imidazole hairpin polyamides are small aromatic rings that typically select the minor groove of DNA and make the DNA molecule more stable. Hairpin polyamides can recognize the minor groove of DNA without exposing it to denaturation. Polyamides (PAs) have gained interest because of arranging gene expression, inhibiting vesicular stomatitis virus (VSV) replication, and their role against human papillomavirus HPV. Since the structure of VSV most likely is an identity RNA duplex in one strand, it has been selected as a prototype virus to test the potential of polyamides for inhibition. Among six sequences of polyamide, only one molecule numbered 1011 showed the ability to control VSV. Based on this fact, we synthesized a novel polyamide that resembles 1011 in its building blocks with an exchange pyrrole ring by imidazole to enhance the interaction between polyamide and genomic protein of VSV. All negative-strand RNA viruses have the same RNA structure in the nucleocapsid and that makes the polyamides a good target for negative-strand RNA viruses, such as respiratory syncytial virus and Ebola virus.