Development of human apurinic/apyrimidinic endonuclease (APE1) inhibitors for cancer therapy


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Mohammed Mohammed, Charles Laughton, Lodewijk Dekker, Peter Fischer, Rachel Abbots,Poulam Patel, Madhusudan Srinivasan

University of Nottingham, UK

Abstract

Potentially cytotoxic AP sites are obligatory intermediates in base excision repair carried out by APE1. A pilot study using fluorescence-based high through-put screening, biochemical and cellular investigations identified a compound that selectively inhibited the DNA repair domain of APE1 and potentiated the cytotoxicity of temozolomide (TMZ). To identify drug-like leads, we then adopted an industry-standard high through-put virtual screening strategy. The Sybyl8.0 molecular modelling software suite was used to build inhibitor templates based on our first generation inhibitors. Similarity searching strategies were then applied to extract pharmacophorically related subsets of compounds from a chemically diverse database of 2.6 million compounds. The compounds in these subsets were then 3D-encoded, energy-minimised, and subjected to docking against the active site of the APE1model, using the genetic algorithm-based programme GOLD2.7. Predicted ligand poses were ranked on the basis of several scoring functions. The top 150 virtual hits with promising pharmaceutical properties underwent detailed in vitro analyses using fluorescence-based APE1 and endonuclease IV (endo IV) cleavage assays and quenching assays. Of the hits, 14/150 were selective and potent APE1 inhibitors (IC50:1- 10 M), 6/150 were potent APE1 inhibitors and showed partial inhibition of endo IV, 3/150 were potent APE1 and endo IV inhibitors. Current evidence using pure APE1 inhibitors suggests potentiation of TMZ toxicity. Further studies are currently underway in melanoma, pancreatic and glioma cancer cell line models.