The four oncogenes, c-MYC, bcl-2, VEGF, and HIF-1a, all contain polyG/polyC tracts in their promoter regions critical for transcriptional activation. The occurrence of DNA G-quadruplex secondary structures has been demonstrated in the promoter regions of these four oncogenes and has been shown to be a transcriptional modulator. While the DNA G-quadruplexes are promising new drug targets, the evaluation of their potential as cancer therapeutic targets depends on the understanding of biologically relevant G-quadruplex structures. Our preliminary studies have allowed us to identify the predominant forms of G-quadruplexes in the promoter regions of c-MYC, bcl-2, VEGF, and HIF-1a, which appear to represent three different basic G-quadruplex structures with VEGF/HIF-1a G-quadruplexes being the same basic type. The different molecular structures of the promoter G-quadruplexes make these structures attractive targets for pathway-specific drug design. In this proposal we intend to define the specific molecular structure of each G-quadruplex and its drug-complex(es). The structural information obtained will be correlated with the biological data to understand the effective gene modulation. Insight into the structures of the promoter G-quadruplexes and their drug complexes will provide an important basis for structure-based rational drug design. We will test our hypothesis that each promoter G-quadruplex can be specifically targeted by different small molecule drug compounds. In addition to the principle that selectivity can be achieved by interactions with different G-quadruplex core structures, we expect that selectivity can also be achieved by interactions within the external loops and capping structures in which binding pockets are generated. Proof of principle will be important in this regard. We will use a combination of NMR, CD, molecular modeling, and microcalorimetry data in concert with appropriate mutant promoter elements. Our primary approach, high field NMR spectroscopy, represents a major tool for structure determination of biologically relevant G-quadruplexes, due to the difficulty of crystallization of such structures. Our ultimate objective is to use a structure-based approach to rationally design small molecule G-quadruplex-interactive compounds that specifically target the G-quadruplex structure unique to each promoter and modulate gene transcription. Specifically, we plan to 1) determine the molecular structure of the biologically relevant G-quadruplex formed in the promoter region of c-MYC and its drug interactions;2) determine the molecular structure of the biologically relevant G-quadruplex formed in the promoter region of bcl-2 and its drug interactions;and 3) determine the molecular structure of the biologically relevant G-quadruplex formed in the promoter region of VEGF/HIF-1a and its drug interactions.
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