Modulating c-Myc transcription by G-quadruplex-interactive small molecules

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DESCRIPTION (provided by applicant): Modulating c-MYC Transcription by G-quadruplex-interactive Small Molecules DNA G-quadruplex secondary structures have recently been found to form in proximal promoter regions as transcriptional regulators, and are considered as a new class of molecular targets for anticancer drugs. Specifically, c-MYC, one of the most commonly deregulated genes in human cancers, has a DNA G-quadruplex motif in the promoter Nuclease Hypersensitive Element (NHE) III1 which regulates 80-95% of its total transcription. The DNA G-quadruplex formed in the c-MYC NHE III1 has been shown to be a transcriptional silencer element; compounds that bind to and stabilize the G-quadruplex conformation can reduce c-MYC expression and are anti- tumorigenic. We have recently discovered that the NM23-H2 protein unfolds the c-MYC promoter G-quadruplex to activate gene transcription. However, although the c-MYC promoter G-quadruplex is the first and most extensively studied system, little is known about its molecular interactions with small molecules and proteins. The hypothesis to be tested is that the physiological functions of c-MYC G-quadruplex-interactive compounds are mediated through not only the G-quadruplex but also the G-quadruplex-interactive protein. We have identified an Ellipticine analog as our lead compound for further optimization to target the c-MYC promoter G- quadruplex. Ellipticine has good "drug-like" properties and has been shown to selectively bind the c-MYC G-quadruplex. We will use NMR to understand the molecular interactions with the c- MYC G-quadruplex and ITC to characterize the thermodynamic contributions of drug binding (Aim 1). Based on this information, we will rationally design and synthesize new Ellipticine analogs with various substituents at C9, N2, N6, and C3 positions (Aim 2). We will use biochemical, biophysical, and biological assays to examine the effects of the Ellipticines on inhibiting NM23-H2 binding and unfolding of the c-MYC G-quadruplex and their effectiveness in c-MYC transcriptional suppression. A combination of structural and biological studies will allow us to understand the specific G-quadruplex interactions of Ellipticine that lead to inhibition of the NM23-H2 protein and suppression of c-MYC transcription. The overall objectives of this research are to establish the structure-activity relationship and underlying molecular mechanism of Ellipticines for c-MYC suppression and to design/synthesize new analogs for further drug development. The specific aims are: 1) To determine structural and thermodynamic details of molecular interactions of Ellipticines and related molecules with the c-MYC G- quadruplex. 2) To design and synthesize new C9-, N2-, N6-, and C3-substituted Ellipticine analogs and to study structure-activity relationship (SAR) of Ellipticines targeting the c-MYC G- quadruplex. 3) To determine how Ellipticine analogs modulate NM23-H2 binding and unfolding of the c-MYC G-quadruplex, and how this correlates with c-MYC transcriptional suppression.