A Structure Activity Relationship Study of Novel DNA-PK Inhibitors

Abstract

Radiotherapy causes DNA double strand breaks (DSB) in cancer cells which can be repaired by non-homologous end joining (NHEJ). DNA-PK is an enzyme that plays an important role in the process of NHEJ, thus inhibition of DNA-PK can result in fewer DSB being repaired and subsequently sensitise cells to radiation. To study the structure activity relationship (SAR) of novel DNA dependent protein kinase (DNA-PK) inhibitors, two series of analogues based on the 3,4-dihydropyrimido[4,5-d]pyrimidin-2(1H)-one and pteridin-7(8H)-one structural cores were designed. Seven 3,4-dihydropyrimido[4,5-d]pyrimidin-2(1H)-one analogues were accessed in 6 linear steps in 35-72% overall yield. Initially, we proposed a 4 linear step route to access the pteridin-7(8H)-one analogues, however, the key ring-closure proceeded in poor yield. We developed a revised route which was also able to deliver these analogues in 4 steps in 21-42% overall yield. All compounds were assessed for authenticity and purity by standard methods. Inhibition of DNA-PK was assessed in a biochemical enzyme inhibition assay. Further, inhibition of PI3Kα and mTOR (representative of the PI3K and PIKK enzyme families) was assessed to explore the selectivity of these compounds. All analogues were also tested as radiosensitizers in UT-SCC-54C head and neck squamous carcinoma cells. In general, most of the new compounds showed good DNA-PK inhibition activity (IC50 < 200 nM), pteridin-7(8H)-one 2.5f was the most potent DNA-PK inhibitor and this translated to radiosensitization with IC50 and S50 values of 1.7 nM and 320 nM, respectively. Comparison of the S50 value determined in the radiosensitization assay and the associated IC50 for PI3Kα and mTOR inhibition showed that most of the compounds would inhibit at least one enzyme other than DNA-PK at S50 concentration. Therefore, further study is still required to increase the selectivity of the compounds for DNA-PK over the PI3K and PIKK families.