Investigation about non-canonical G-quadruplex stabilization as an alternative approach to PARP1 inhibition

PARP1 is a nuclear enzyme involved in DNA repair processes. Since its inhibition causes sensitization to DNA damaging chemotherapy (the so-called “synthetic lethality”), several inhibitors have been recently developed and exploited for clinical use. However, the emergence of resistance to PARP1 inhibitors increased the interest towards alternative approaches able to interfere with PARP1 activity. In particular, the promoter region of PARP1 gene was mapped and a characteristic, non-canonical G-quadruplex-forming sequence was identified. A strong correlation between G-quadruplex stabilization in gene promoters and transcriptional regulations has been proposed for several oncogenes. Since no PARP promoter modulators have been identified so far, we were intrigued by the possibility that appropriately designed molecules could allow PARP1 inhibition by a different mechanism. In fact, stabilization of G4 of the promoter region could cause an upstream down-regulation of PARP1 itself and a consequent, less efficient answer to DNA damage in cancer cells. Given the peculiar characteristics of PARP1 G4, its interaction with a small collection of G4 binders was investigated, taking in account that a variegated structural diversity could be helpful in the rationalization of the key molecular features required for an effective binding. Six compounds, extensively studied and known for showing great affinity towards canonical G4, were selected and NMR, CD, and fluorescence titration studies were carried out. The obtained results demonstrated that widely functionalized flat molecules with flexible chains were not able to perturbate nor stabilize the structure; whereas planar, more compact, and less extended systems demonstrated to establish specific interactions with the external G-tetrads. These results confirm that the structural requirements for an optimal interaction between the ligand and this peculiar G4 portion are quite strict. Nonetheless, this could be considered as a key starting for the identification and characterization of ligands able to selectively interact with the PARP promoter G4.