A first-in-class clinical G-quadruplex-targeting drug. The bench-to-bedside translation of the fluoroquinolone QQ58 to CX-5461 (Pidnarulex)

by Selleckchem | Mar 28 2023

CX-3543 (Quarfloxin) and CX-5461 (Pidnarulex) were originally derived from a group of fluoroquinolones that were shown to have dual topoisomerase II (Top2) and G-quadruplex (G4) interactions, and QQ58 was the starting structure for their design. Quarfloxin was initially shown to inhibit c-MYC mRNA expression. Studies at Cylene Pharmaceuticals showed that the primary mechanism of action of Quarfloxin is due to displacement of nucleolin from quadruplexes on the non-template strand of rDNA, causing rapid redistribution of nucleolin from nucleoli, inhibition of rRNA synthesis, and apoptotic death in cancer cells. At Cylene a follow-up compound to Quarfloxin, named Pidnarulex (CX-5461), was optimized for targeting RNA Pol 1. Significantly, in more recent work published in Proc Natl Acad Sci USA and Cell in 2020 and in eLIFE and Nat Comm in 2021, it has been shown that the real molecular target for Pidnarulex is Top2 at transcribed regions containing G4s, rather than RNA Pol 1. These results support the original design strategy published in Mol Cancer Ther in 2001, which was to rationally design a G4-targeting drug (QQ58) starting from a fluoroquinolone duplex-targeting Top2 poison (A-62176) that had good drug-like properties. A very important breakthrough was realized when homologous recombination (HR) was found to be important in the repair of DNA damage caused by G4-interactive compounds, suggesting that a synthetic lethal approach might be useful in identifying cancer patients sensitive to these agents. Through use of an unbiased screen, this mechanistic insight was shown to directly apply to Cylene compounds, which were found to induce DNA damage and to be dependent on BRCA1/2-mediated HR and the DNA-PK-mediated nonhomologous end-joining (NHEJ) pathway for damage repair. To evaluate how this mechanistic insight involving a synthetic lethal approach might be applied clinically, a recent Canadian Phase I clinical trial with Pidnarulex in breast and ovarian cancer patients with known BRCA1/2 germline mutations was carried out. Because of the G4 stabilizer function of Pidnarulex, patient populations that responded well to this compound were identified: they are cancer patients with BRCA1/2 deficiency or deficiency in other DNA damage response pathways. Clinically observed resistance to Pidnarulex resulted from reversion to WT BRCA2 and PALB2 ("partner and localizer of BRCA2," because it partners with another gene, called BRCA2), thus providing strong evidence for the underlying synthetic lethal hypothesis proposed for G4-targeting compounds that cause DNA damage.

Comments：

The discovery that Pidnarulex targets topoisomerase II at transcribed regions containing G-quadruplexes, rather than RNA Pol 1, is a significant finding that supports the original design strategy of these compounds. The identification of homologous recombination (HR) as an important pathway for the repair of DNA damage caused by G-quadruplex-interactive compounds, and the subsequent use of synthetic lethality to identify cancer patients who may benefit from these agents, is also a promising approach in cancer therapy.

The results of the Canadian Phase I clinical trial with Pidnarulex in breast and ovarian cancer patients with BRCA1/2 germline mutations provide further evidence for the synthetic lethality hypothesis and suggest that patients with BRCA1/2 deficiency or deficiency in other DNA damage response pathways may be particularly sensitive to this compound. The observation of resistance resulting from reversion to WT BRCA2 and PALB2 highlights the importance of continued research into the mechanisms underlying the response and resistance to G-quadruplex-targeting compounds.