Abstract 1829: Small molecule stabilization of the kRAS promoter G-quadruplex as a target for novel pancreatic cancer therapeutics

Abstract

Abstract kRAS is one of, if not the, most prevalent oncogenic aberrations identified to date. It is either upregulated or mutationally activated in a multitude of cancers, including close to 100% of pancreatic adenocarcinomas. Pancreatic cancer carries the highest mortality rate of all cancers, with only a 3-6 month median survival, and a 5-year survival of <5%. There is a desperate need for new therapeutics, particularly those targeting kRAS. This is not a new concept; due to the common nature of the kRAS mutation a significant effort has been made to develop drugs that target its activated form. However, the clinical activity of those drugs has been disappointing due to a variety of mechanistic hurdles. The presented works describe a novel target to downregulate kRAS expression - secondary structures within the proximal promoter, which contains a unique string of G-rich DNA. Negative superhelicity induced by transcription results in this region opening up to form unique secondary structures called G-quadruplexes (G4s). These G4s most often act as silencer elements, forming globular structures that mask binding sites for transcriptional factors, allowing for specific molecular targeting by small molecule drugs, modulating transcription, and protein expression. Using the confirmed major isoform - a unique ‘kinked’ structure - as the primary target, we undertook a screening effort in order to identify potential G4-stabilizing small molecules. Several hundred compounds were screened, and two chemical classes consistently emerged: ellipticines (E) and quindolines (Q). The lead compounds from each pharmacophore are NSC176327 (E-14) and Quindoline i (Q-i), respectively, each of which has previously been demonstrated to stabilize other G4 structures (such as the parallel structure found within the MYC promoter.) What is most intriguing is the clear difference in isoform stabilization with these compounds; E-14 stabilizes the major kinked isoform, whereas Q-i is a bit more promiscuous and stabilizes several isoforms as demonstrated by FRET melt, the Polymerase Stop Assay and DMS footprinting. Both of these compounds demonstrate cytotoxicity, as measured by MTS, at 24 and 72 h, in a variety of pancreatic cell lines, with E-14 being notably more potent. Cytotoxicity is is being correlated to changes in kRAS mRNA expression. G4s have emerged as a potential DNA target with great potential for specificity as they are more globular than nascent DNA, and each carry some degree of distinctiveness. Using the kRAS proximal promoter G4 structure as the primary target, a drug discovery program will have great potential to develop a potent, specifically targeted small molecule to be used in the treatment of pancreatic adenocarcinomas, as well as childhood leukemias, ovarian, lung, and colon cancers. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1829. doi:1538-7445.AM2012-1829