Abstract LB239: Overcoming resistance to camptothecin-based topoisomerase I inhibitors through a novel core scaffold design strategy

Abstract Camptothecin (CPT) derivatives as DNA topoisomerase I (TOPO-1) are widely used to treat various cancers. However, their clinical efficacy was significantly undermined by both inherent resistance and the rapid development of emerging resistance. Although resistance mechanisms are complicated, some key factors are identified such as TOPO-1 mutations and drug efflux. Unfortunately, all clinical stage CPT-derived TOPO-1 inhibitors shared the original CPT core structure, thus little chance to address resistance via structural diversity. In this study, we aimed to discover a novel class of non-CPT core TOPO-1 inhibitors that specifically address the key enzyme mutations thus overcoming resistance to current TOPO-1 drugs in the clinic. Using a Computer-Assisted Drug Design (CADD) approach, a non-CPT core scaffold was designed to specifically improve binding to the clinically relevant R364H mutant. Molecules from the novel scaffold performed very well in our computational model showing significantly improved hydrogen bonding and polar interactions with both wild type and R364H mutated TOPO-1. Cellular assay proved that molecules with predicted enhancements led to a 30-fold improvement in inhibitory potency compared to topotecan in the R364H-mutant cell line. Furthermore, the novel compounds exhibited markedly reduced efflux in the BCRP-overexpressing cell lines, maintaining higher intracellular concentrations and thereby enhancing their anticancer activities. More importantly, compared to irinotecan these molecules demonstrated 50 to 1000-fold higher potency in patient-derived, irinotecan-resistant tumor organoid models, thus successfully addressed tumor resistance to current TOPO-1 inhibitors. In vivo antitumor activity was also validated in various PD animal models. A PCC molecule was identified and moved into IND-enabling development, which shows significant promise as next-generation therapies for cancers overcoming resistant to traditional TOPO-1 inhibitors. Recent breakthrough discoveries of ADCs attracted more attention to TOPO-1 inhibitors, however most if not all payloads targeting TOPO-1 still utilized the original CPT core (e.g. DXD, SN-38). Therefore, it is anticipated that ADC treatment will lead to new resistance, and our novel molecules with a non-CPT core could address future resistance via structure diversity. Citation Format: Xiaodan Fu, Yaozong Li, Qilin Wang, Hui Liu, Dongmei Hu, Qun Dang. Overcoming resistance to camptothecin-based topoisomerase I inhibitors through a novel core scaffold design strategy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr LB239.