Abstract 4794: Oligoamide-based mimics of double-stranded B-DNA as a new class of DNA topoisomerase I catalytic inhibitors
Authors: Pourquier Philippe , Ziach Krzysztof , Chollet Céline , Parissi Vincent , Marchivie Mathieu , Prabhakaran Panchami , Bose Partha P. , Laxmi-Reddy Katta , Godde Frédéric , Chaignepain Stéphane , Schmitter Jean Marie , Huc Ivan 
Published: July 2016

Abstract
Since the discovery of Topoisomerase I as a specific target for the treatment of cancers more than 30 years ago, only two inhibitors derived from the natural compound camptothecin (CPT) have been approved in the clinic for the treatment of colon, lung and ovarian cancers: topotecan and irinotecan. The cytotoxicity of these Top1 poisons relies on their capability to stabilize covalent Top1-DNA complexes, leading to replication-mediated DNA double-strand breaks. However tumor cells develop multiple resistance mechanisms that are limiting their efficacy. Though new CPT derivatives and other Top1 poisons with various chemical structures have been developed, they share the same resistance mechanisms. Aside from conventional approaches focus on compounds with higher potency to stabilize Top1-DNA complexes, we investigated the possibility to inhibit Top1 binding to DNA and/or DNA cleavage by using DNA mimics that would act as decoys, a strategy that was never explored before. To this aim, single chain oligoamides composed by iteration of mQQ units (Q: 8-amino-2-quinoline carboxylic acid; mQ: 8-aminomethyl-2-quinoline carboxylic acid) were synthesized. These molecules fold into helices that are stabilized by electrostatic repulsions and hydrogen bonds between the amide functions and endocyclic nitrogen atoms at adjacent residues. When Q and mQ precursors are functionalized by negatively charged residues, the positions of these residues in the folded structure match the position of phosphate residues in duplex B-DNA. Because distances between residues in mQQ and QmQ units are slightly different, it is possible to define a major groove and a minor groove, as in B-DNA, with the possibility to impact on groove width by changing the positions of the substituents (Q4 or Q5 for substitution in position 4 or 5 of the quinoline monomer, respectively), clearly establishing (mQQ5)n and (mQQ4)n as potential DNA-mimics of an unprecedented kind.
We found that both (mQQ5)n and (mQQ4)n oligomers inhibited the activity of Top1-mediated relaxation of supercoiled DNA in vitro. Inhibition increased with the length of the oligoamide to reach an IC50 value (concentration inhibiting 50% of Top1-mediated DNA relaxation) around the nM range for the longest oligomer that was tested i.e. (mQQ4)16, corresponding to a double-strand DNA of 16 base pairs. By comparison, CPT had an IC50 of ∼10 μM in the same conditions. Top1 inhibition was rather selective as a (mQQ4)8 oligomer moderately inhibited Top2-mediated activity and did not affect the activity of various DNA interacting enzymes such as restriction enzymes XhoI and NdeI or nucleases such as DNAse I, S1 nuclease, benzonase or Flap-endonuclease I. Because these oligomers are resistant to proteases and nucleases and can be synthesized rapidly by solid phase synthesis with the possibility to modify its substituents without altering their helicity, they represent good candidates for drug development.
Citation Format: Philippe Pourquier, Krzysztof Ziach, Céline Chollet, Vincent Parissi, Mathieu Marchivie, Panchami Prabhakaran, Partha P. Bose, Katta Laxmi-Reddy, Frédéric Godde, Stéphane Chaignepain, Jean Marie Schmitter, Ivan Huc. Oligoamide-based mimics of double-stranded B-DNA as a new class of DNA topoisomerase I catalytic inhibitors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4794.