Abasic sites are ubiquitous DNA lesions that are mutagenic and cytotoxic but are removed by the base excision repair pathway.
DNA polymerase β carries out two of the four steps during base excision repair, including a
lyase reaction that removes the abasic site from
DNA following incision of its 5'-phosphate.
DNA polymerase β is overexpressed in
cancer cells and is a potential anticancer target. Recently,
DNA oxidized abasic sites that are produced by potent
antitumor agents were shown to inactivate
DNA polymerase β. A library of small molecules whose structures were inspired by the oxidized abasic sites was synthesized and screened for the ability to irreversibly inhibit
DNA polymerase β. One candidate (3a) was examined more thoroughly, and modification of its
phosphate backbone led to a molecule that irreversibly inactivates
DNA polymerase β in
solution (IC50 ≈ 21 μM), and inhibits the
enzyme's
lyase activity in cell lysates. A bisacetate analogue is converted in cell lysates to 3a. The bisacetate is more effective in cell lysates, more cytotoxic in
prostate cancer cells than 3a and potentiates the cytotoxicity of
methyl methanesulfonate between 2- and 5-fold. This is the first example of an irreversible inhibitor of the
lyase activity of
DNA polymerase β that works synergistically with
a DNA damaging agent.