Development of Novel DNA Binding HIV-1 Integrase Inhibitors

Clay Wang, USC, Los Angeles
Biomedical and Clinical Sciences

Background: Nature continues to provide a rich source of compounds that can inhibit HIV infection or modulate specific molecular targets associated with viral entry or replication. In this pilot study, a biosynthetic mechanism based production system will be developed to create analogs of the depsipeptide echinomycin and triostin and evaluate the new chemical entities for biological activity against HIV-1 integrase. The subject of this project echinomycin is a member of the quinoxaline natural products characterized by its C2 symmetric cyclic depsipeptide structure. A general feature of quinoxaline natural products is the bicyclic chromophores that allow the quinoxaline antibiotics to bisintercalate into DNA. Members of the quinoxaline antibiotics differ by the nature of the peptide backbone and the functional groups found on the DNA intercalating quinoxaline chromophore. Interestingly two members of the quinoxaline antibiotics, quinoxapeptin A and luzopeptin A are known HIV reverse transcriptase inhibitors. Our interest in quinoxaline antibiotics as HIV integrase inhibitors stems from earlier reports with lexitropsin and pyrrole imidazole polyamides demonstrating that DNA binding small molecules are potent HIV-1 integrase inhibitors.

Methods: The innovative aspect of this project is that we will biosynthesize novel "nonnatural" natural products using a strain of Escherichia coli (E. coli) that that has been bioengineered to heterologously express echinomycin and triostin biosynthesis genes isolated from the original producing streptomyces. By targeted manipulation of the natural product biosynthetic path-ways, analogs with new structural features not otherwise found in nature can be produced. Since the whole process is biosynthetic, production scale up can be achieved by increasing the size of the bacterial culture.
Preliminary Results: In this abstract we will be presenting only our preliminary results. In our preliminary studies, we have developed strains of E. coli that harbor plasmids containing the biosynthetic gene for either triostin or echinomycin. A high-density fermentation system has also been developed to produce triostin and echinomycin in amounts necessary for NMR and LC/MS characterizations. We also found that the natural echinomycin is a HIV-1 integrase inhibitor at 10M. In the next two years we plan to develop new HIV-1 integrase inhibitors by leveraging the biosynthetic system we have developed.

Conclusions: DNA binding molecules such as echinomycin can inhibit HIV-1 integrase and the platform is set to make analogs of these DNA binding molecules in a biosynthetic fashion.