Abstract 4930: Foldamers mimicking the B-DNA surface as a new class of DNA topoisomerase I inhibitors

Abstract

DNA mimicry has been the subject of intensive research and resulted in the development of DNA analogues such as PNAs and LNAs. There are also examples of proteins with structural and/or charge distribution analogies with respect to the DNA double helix which allow them to interfere with other DNA-binding proteins and modulate the biological processes in which they are involved. We previously characterized a new class of DNA-surface mimic molecules constituted by repetitions of dimeric units of 8-amino-2-quinolinecarboxylic acid (Q) and 8-aminomethyl-2-quinolinecarboxylic acid (mQ). The helical folding of these entities can mimic a B-DNA molecule, displaying a minor and a major groove that can be modulated depending on the dimers and of the nature of their side chains. In vitro, these DNA mimics could inhibit, in a relative selective manner, the catalytic activity of DNA topoisomerase I (Top1), whereas they had no effect on the activity of DNA polymerases or DNAses. Inhibition of Top1-mediated relaxation of supercoiled DNA plasmid increased with the length of the DNA mimics. Here, we further characterized the mechanism of Top1 inhibition by these DNA mimics. We found that, conversely to camptothecin (CPT) and its derivatives that poison Top1 via the inhibition or the re-ligation step of the reaction, DNA mimics inhibited Top1-mediated DNA cleavage in vitro by preventing the binding of the enzyme to its substrate, a mechanism of Top1 competitive inhibition that was formerly referred to as catalytic inhibition. We also found that co-incubation of DNA mimics with CPT had an additive effect on the inhibition of Top1-mediated relaxation of supercoiled DNA, further suggesting a mechanism that is different from CPT. Because transfection of DNA mimics could inhibit the growth of various cancer cell lines, we further investigated whether Top1 could play a role in this cytotoxicity. We found that Top1 knock-down in OVCAR4 ovarian cancer cells resulted in decreased sensitivity to the (mQQ4)8 DNA mimic as compared to OVCAR4 control cells, suggesting that Top1 is a target of DNA mimics in cells and is involved in their cytotoxic effects. Conversely to CPT, transfection of HCT116 cells with the (mQQ4)8 DNA mimic was not associated with an increase in γH2AX, suggesting that DNA mimics do not induce DNA breakage. We are currently analyzing whether the (mQQ4)8 can have an impact on CPT-induced Top1-DNA complexes formation. Interestingly, we also showed that several SN38-resistant HCT116 cell clones characterized by specific Top1 mutations were still sensitive to the (mQQ4)8 DNA mimic. Together our results demonstrate that DNA mimics can be considered as a new class of competitive inhibitors of Top1. Further studies are ongoing to identify the structural features that are essential for Top1 inhibition in order to generate more potent derivatives that could be used to counteract resistance to CPT derivatives used in the clinic. Citation Format: Aurélie Garcin, Valentina Corvaglia, Madeleine Bossaert, Marie-Jeanne Pillaire, Ivan Huc, Sébastien Britton, Vincent Parissi, Philippe Pourquier. Foldamers mimicking the B-DNA surface as a new class of DNA topoisomerase I inhibitors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4930.