Structural Basis for Specificity of Common PARP and Tankyrase Inhibitors

Inhibitors of poly(ADP-ribose) polymerase-1 (PARP1) and tankyrases are promising agents in therapeutics development for several cancers and ischemia, and common tools in studying DNA repair and signaling pathways. Ten human PARP family enzymes and seven widely used PARP inhibitors were studied using enzymatic assays and X-ray crystallography. PARP inhibitors are generally profiled in vitro using PARP catalytic domain fragments. Meanwhile, PARP enzymes are multidomain proteins and we show that full length PARP1 enzyme, and several of its closest isoforms, catalyze poly-ADP-ribosylation up to 200-fold more efficiently than their catalytic fragments do. Further, we find that using only catalytic domain fragments instead of full length PARP1 and -2 enzymes leads to misinterpretation of IC50 values by a factor of ~10. Veliparib is the most selective PARP1/2 inhibitor of five clinical PARP inhibitors. PJ34 and Rucaparib are the broadest PARP inhibitors of the seven compounds. The reportedly selective tankyrase inhibitor XAV939, known for its effects on the Wnt pathway, inhibits PARP1 and -2 with nanomolar IC50 values. Crystal structures of these inhibitors in complex with various PARP family members illustrate the molecular basis for broad vs. selective PARP inhibition. Our PARP inhibitor profile provides important guidelines both for future experimental design and for re-interpretation of previously obtained results.