The kinase polypharmacology landscape of clinical PARP inhibitors

Abstract

Polypharmacology plays an important role in defining response and adverse effects of drugs. For some mechanisms, experimentally mapping polypharmacology is commonplace, although this is typically done within the same protein class. Four PARP inhibitors have been approved by the FDA as cancer therapeutics, yet a precise mechanistic rationale to guide clinicians on which to choose for a particular patient is lacking. The four drugs have largely similar PARP family inhibition profiles, but several differences at the molecular and clinical level have been reported that remain poorly understood. Here, we report the first comprehensive characterization of the off-target kinase landscape of four FDA-approved PARP drugs. We demonstrate that all four PARP inhibitors have a unique polypharmacological profile across the kinome. Niraparib and rucaparib inhibit DYRK1s, CDK16 and PIM3 at clinically achievable, submicromolar concentrations. These kinases represent the most potently inhibited off-targets of PARP inhibitors identified to date and should be investigated further to clarify their potential implications for efficacy and safety in the clinic. Moreover, broad kinome profiling is recommended for the development of PARP inhibitors as PARP-kinase polypharmacology could potentially be exploited to modulate efficacy and side-effect profiles.

Figure 1

Chemical structures and known PARP activities of FDA-approved PARP inhibitors. (a) Chemical structures of the four FDA-approved PARP drugs. The benzamide core pharmacophore shared by all clinical PARP inhibitors is highlighted in bold with orange shading. The rest of the chemical structure that is not shared between the inhibitors and confers them with different size and flexibility has grey shading. (b) Known target profile of clinical PARP inhibitors across members of the PARP enzyme family. IC₅₀ values are obtained from the literature and the ChEMBL database (www.ebi.ac.uk/chembl/) and ranges are given where there is more than one published value^,.

Figure 2

Kinome profiling of the four FDA-approved PARP inhibitors across 392 unique human kinases and 76 mutated, atypical and other forms. This was carried out using the in vitro binding platform of DiscoveRx’s KinomeScan®. The assays were perfomed at a single 10 μM concentration. The TREEspot™ representations of the kinome tree, with superimposed in vitro binding data for each PARP inhibitor, illustrate how rucaparib and niraparib bind to a significant number of kinases while talazoparib only modestly binds to two kinases and olaparib does not bind to any of the kinases tested. The chemical structures of the PARP drugs are included and their different R-groups highlighted in blue shading to illustrate different side-chains that may influence polypharmacology.

Figure 3

Concentration-response curves for the most potent kinase off-target interactions of clinical PARP inhibitors. (a) concentration-response curves and IC₅₀ calculation of the most potent interactions in the in vitro binding assay (see Methods) of niraparib (top) and rucaparib (bottom) analysed in triplicate using Reaction Biology’s HotSpot radiometric assay that directly measures kinase catalytic activity. (b) concentration-response curve and EC₅₀ calculation for rucaparib against CDK16 and niraparib against DYRK1A using a target-engagement cellular assay based on NanoBRET technology and an optimized set of cell-permeable kinase tracers (see Methods for details). Olaparib was used as a negative control. The target engagement cellular assays were performed in quadruplicate (two technical repeats in each of two independent experiments). (c) table summarising the calculated IC₅₀ and EC₅₀ values for the kinase off-targets DYRK1B, CDK16, PIM3 and DYRK1A.

Figure 4

The nineteen differential adverse reactions between FDA-approved clinical PARP inhibitors. Data were extracted from the FDA prescribing information and published results of the largest clinical trials. Side-effect frequencies are not considered due to the differences between the cut-offs used in each trial and FDA prescribing information for each PARP inhibitor (see Methods for details). Each adverse reaction considered common for at least one PARP drug and not identified for at least another PARP inhibitor is represented as a circle. The circles are coloured according to the drugs that present this adverse reaction in their prescribing information or publication of their largest clinical trial.