Structural Basis for Potency and Promiscuity in Poly(ADP-ribose) Polymerase (PARP) and Tankyrase Inhibitors

Abstract

Selective inhibitors could help unveil the mechanisms by which inhibition of poly(ADP-ribose) polymerases (PARPs) elicits clinical benefits in cancer therapy. We profiled 10 clinical PARP inhibitors and commonly used research tools for their inhibition of multiple PARP enzymes. We also determined crystal structures of these compounds bound to PARP1 or PARP2. Veliparib and niraparib are selective inhibitors of PARP1 and PARP2; olaparib, rucaparib, and talazoparib are more potent inhibitors of PARP1 but are less selective. PJ34 and UPF1069 are broad PARP inhibitors; PJ34 inserts a flexible moiety into hydrophobic subpockets in various ADP-ribosyltransferases. XAV939 is a promiscuous tankyrase inhibitor and a potent inhibitor of PARP1 in vitro and in cells, whereas IWR1 and AZ-6102 are tankyrase selective. Our biochemical and structural analysis of PARP inhibitor potencies establishes a molecular basis for either selectivity or promiscuity and provides a benchmark for experimental design in assessment of PARP inhibitor effects.

PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes

“…In a recent screen with different PARPis, the Schuler group (Thorsell et al 2016) tested the capability of each inhibitor to specifically attenuate the in vitro catalytic activity of a panel of PARPs. Furthermore, they used X-ray crystallography to elucidate the mechanisms of action for the different PARPis.…”

“…Using this strategy, they assayed 11 members of the PARP family, including PARP-1, PARP-2, and PARP-3, and the Tankyrases. They were able to determine that inhibitors such as veliparib and niraparib have the highest selectivity for PARP-1 and PARP-2, whereas other inhibitors, such as olaparib, have a high potency but relatively lower selectivity for PARP-1 and PARP-2 (Thorsell et al 2016). This study not only provides critical information regarding selectivity and potency of different clinically used PARPis but also establishes assays that can be used in the future to test new PARPis.…”

“…For example, the CETSA was able to distinguish between olaparib, a well-characterized PARP-1 inhibitor that binds directly to PARP-1, and iniparib, a proposed PARP-1 inhibitor that reached phase III clinical trials but showed no efficacy (Martinez Molina et al 2013). Similarly, CETSA was used to assess the inhibitory potential of the Tankyrase inhibitor XAV939 toward PARP-1 ( Thorsell et al 2016). The structural differences revealed for different PARPs-for example, PARP-1 and PARP-3-have also been used to assess the selectivity of different inhibitors (Lehtio et al 2009).…”

Small-Molecule Inhibitors Targeting DNA Repair and DNA Repair Deficiency in Research and Cancer Therapy

“…An in vitro study conducted on a series of 185 small-molecule PARP inhibitors and the catalytic domains of 13 out of 17 human PARP enzymes suggested a potential promiscuous binding to several PARP family members for even such clinically successful inhibitors as olaparib and rucaparib (Wahlberg et al, 2012). Niraparib and veliparib , on the other hand, have over 100-fold specificity for PARP1 and PARP2 over other PARP enzymes (Thorsell et al, 2017). Figure 3 shows one of the determinants for such selectivity – niraparib binds within the nicotinamide binding pocket in the ADP-ribosyl transferase catalytic site and also makes contacts with the regulatory subdomains of PARP1 and PARP2 (E763 & D766 in PARP1).…”

“…The overlap of a nicotineamide analog DHQ (green; PDB 1PAX) bound to the active site of PARP1 and the second generation PARP1 inhibitor niraparib (light blue; PDB 1PAX), which occupies both the nicotinamide-ribose binding pocket and the adenosine-ribose binding pocket of ADP-ribosyl transferase catalytic site, making additional contacts with E763 and D766 of the regulatory α-helical sub-domain (HD) (Thorsell et al, 2017). PARP1 ADP-ribosyl transferase catalytic domain (CAT; PDB 1PAX) is shown as a surface representation.…”