Allosteric regulation of DNA binding and target residence time drive the cytotoxicity of phthalazinone-based PARP-1 inhibitors

• Published in: Cell chemical biology Vol. 29; no. 12; pp. 1694 - 1708.e10
• Main Authors: Arnold, Moriah R., Langelier, Marie-France, Gartrell, Jessica, Kirby, Ilsa T., Sanderson, Daniel J., Bejan, Daniel S., Šileikytė, Justina, Sundalam, Sunil K., Nagarajan, Shanthi, Marimuthu, Parthiban, Duell, Anna K., Shelat, Anang A., Pascal, John M., Cohen, Michael S.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Ltd 15.12.2022
• Subjects: ADP-ribosylation; Allosteric Regulation; Antineoplastic Agents - pharmacology; Binding Sites; NAD - metabolism; NAD+-competitive inhibitors; PARPs; Poly(ADP-ribose) Polymerase Inhibitors - chemistry; Poly(ADP-ribose) Polymerase Inhibitors - pharmacology; target residence time; PARPs; NAD+-competitive inhibitors; allosteric regulation; target residence time; ADP-ribosylation; NAD(+)-competitive inhibitors
• ISSN: 2451-9456; 2451-9448; 2451-9456
• DOI: 10.1016/j.chembiol.2022.11.006

Allosteric coupling between the DNA binding site to the NAD+-binding pocket drives PARP-1 activation. This allosteric communication occurs in the reverse direction such that NAD+ mimetics can enhance PARP-1’s affinity for DNA, referred to as type I inhibition. The cellular effects of type I inhibition are unknown, largely because of the lack of potent, membrane-permeable type I inhibitors. Here we identify the phthalazinone inhibitor AZ0108 as a type I inhibitor. Unlike the structurally related inhibitor olaparib, AZ0108 induces replication stress in tumorigenic cells. Synthesis of analogs of AZ0108 revealed features of AZ0108 that are required for type I inhibition. One analog, Pip6, showed similar type I inhibition of PARP-1 but was ∼90-fold more cytotoxic than AZ0108. Washout experiments suggest that the enhanced cytotoxicity of Pip6 compared with AZ0108 is due to prolonged target residence time on PARP-1. Pip6 represents a new class of PARP-1 inhibitors that may have unique anticancer properties. [Display omitted] •AZ0108 is a type I inhibitor of PARP-1•Type I inhibition induces replication stress•AZ0108 analog synthesis shows that type I inhibition can be finely tuned•The AZ0108 analog Pip6 is a long-residence-time type I inhibitor Arnold et al. identify NAD+-competitive, reverse-allosteric (i.e., type I) inhibitors of PARP-1. These type I PARP-1 inhibitors induce replication stress in tumorigenic cells with no known defects in homologous recombination (HR) distinguishing them from clinical PARP-1 inhibitors. One particular type I inhibitor, Pip6, had a long target, residence time, which profoundly enhanced its cytotoxicity in Ewing sarcoma cells compared with clinical PARP-1 inhibitors.