This project is in collaboration with the laboratory of Dr. Daniel Appella (LBC/NIDDK), which specializes in synthetic chemistry of biomimetics. This is an extension of their work developing hybrids of DNA and Peptide Nucleic Acid (PNA) molecules as programmable scaffolds for the multivalent display of biological ligands. PNAs are oligomeric molecules with peptide-like backbones and nucleic acid-type bases, i.e. the A, G, C &T/U of DNA and RNA, for sidechains. Thus, by adjusting the sequence of the monomers, PNAs can be programmed to bind in a helical conformation to a single or tandem repeated complementary sequence in DNA. Specific ligands are positioned anywhere along the PNA/DNA scaffold by the programmed addition of bridging linkers to the synthesized PNA backbone. For a proof of principle, we focused on the conserved RGD sequence in extracellular matrix proteins that is a preferential ligand of Integrin alphaVbeta3. We used a 5-residue cyclic-peptide analog of this sequence that is similar to the drug Cilengitide (MerckSerono), which is currently under Phase II investigation for Glioblastoma and other cancers. To determine the optimal configuration, the Appella lab generated a library of hybrid molecules with systematically-varied ligand positions and densities, and then screened it on a melanoma cell binding assay. Balancing molecular size and potency, a construct with 5 PNA segments, each presenting three RGD ligands, was judged the optimal inhibitor. Using a radiolabled echistatin displacement assay, this optimal construct was found to bind 400 times stronger to alphaVbeta3 than the monomeric RGD control. Finally, this optimal PNA/DNA inhibitor was also found to outperform monomeric cyclic-RGD in blocking lung metastasis of melanoma cells in a mouse model. A manuscript of this work is currently in review.
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