PARP inhibitors: Synthetic lethality in the clinic

Abstract

PARP inhibitors (PARPi), a cancer therapy targeting poly(ADP-ribose) polymerase, are the first clinically approved drugs designed to exploit synthetic lethality, a genetic concept proposed nearly a century ago. Tumors arising in patients who carry germline mutations in either BRCA1 or BRCA2 are sensitive to PARPi because they have a specific type of DNA repair defect. PARPi also show promising activity in more common cancers that share this repair defect. However, as with other targeted therapies, resistance to PARPi arises in advanced disease. In addition, determining the optimal use of PARPi within drug combination approaches has been challenging. Nevertheless, the preclinical discovery of PARPi synthetic lethality and the route to clinical approval provide interesting lessons for the development of other therapies. Here, we discuss current knowledge of PARP inhibitors and potential ways to maximize their clinical effectiveness.

Fig. 1. Mechanism of action of PARPi.

(A) Schematic of synthetic lethality. In its simplest form, the simultaneous alteration of two genes or proteins (shown here as A and B) causes cell death, whilst alteration of either gene/protein alone does not. When the concept is applied to cancer treatment, where gene A represents an oncogene, tumor suppressor gene or oncogenic process/pathway, gene B, once identified, becomes a candidate therapeutic target that can be used to target tumor cells with dysfunction in A. (B) A model describing the PARP1 catalytic cycle. (i) In its non-DNA bound state, PARP1 exists in a relatively disordered conformation, commonly referred to as “beads on a string” (4). The domain structure of PARP1 is shown, including three Zinc-finger related domains (ZnF 1, 2 and 3), BRCT, WGR and catalytic domain encompassing two subdomains; a helical domain (HD) and an ADP-ribosyltransferase (ART) catalytic domain. In this non-DNA bound state, HD acts as an auto-inhibitory domain preventing binding of the PARP-superfamily co-factor, β-NAD⁺, to its ART binding site (5). (ii) Damage of the DNA double helix often causes the formation of single strand DNA breaks (SSBs, pre-damaged and damaged DNA structures are shown); SSBs cause a change in the normal orientation of the double helix, which in-turn, (iii) provides a binding site for DNA binding PARP1 ZnF domains. The interaction of ZnF 1,2 and 3 with DNA initiates a step-wise assembly of the remaining PARP1 protein domains onto the PARP1/DNA nucleoprotein structure, shown in (iv); this process leads to a change in HD conformation, and resultant loss auto-inhibitory function, thus allosterically activating PARP1 catalytic activity (5). (v) ART catalytic activity drives the PARylation of PARP1 substrate proteins (branched PAR chains are shown on a target protein), mediating the recruitment of DNA repair effectors, chromatin remodelling and eventually DNA repair. (vi) PARP1 autoParylation (likely in cis at SSBs but possibly in trans at other DNA lesions (4)) finally causes the release of PARP1 from DNA and the restoration of a catalytically inactive state (shown in (i)). (viii) Several clinical PARPi, each of which binds the catalytic site, prevent the release of PARP1 from DNA, “trapping” PARP1 at the site of damage, potentially removing PARP1 from its normal catalytic cycle. These images are schematic; detailed structures and models of PARP1/DNA nucleoprotein complexes are described elsewhere [(4, 5) and references therein]. (C) Clinical PARP inhibitors. Chemical structures of five clinical PARPi are shown. The ability of each PARPi to trap PARP1 on DNA differs (talazoparib being the most potent PARP1 trapping inhibitor, veliparib being the least potent) and somewhat correlates with cytotoxic potency (–24). (D) A model of PARP inhibitor synthetic lethality. Trapped PARP1/DNA nucleoprotein complexes impair the progression of replication forks. (i) schematic of trapped PARP1 on DNA in front of a replication fork; newly synthesized DNA is shown in red. (ii) The replication fork is impeded by trapped PARP1. This normally induces a DNA damage response. (iii) Homologous recombination repair (HRR), involving BRCA1 and BRCA2 tumor suppressor proteins, is the optimal DNA repair process for repairing and restarting replication forks stalled by PARPi and also involves the use of additional “BRCAness” proteins (see main text). In the absence of effective HRR, cells use DNA repair processes that can potentially generate large-scale genomic rearrangements, which often leads to tumor cell death and synthetic lethality. (v) Even where HRR is defective, PARPi resistance occurs. Multiple mechanisms cause PARPi resistance, but can be broadly classified into the examples shown (see also main text).

Fig. 2. Clinical PARPi synthetic lethality.

(A) Predictive biomarkers of PARP inhibitor sensitivity. Companion FDA and EMA approved tests, which detect the presence of either germ-line or somatic BRCA1 or BRCA2 mutations, are currently used to identify patients likely to respond to PARPi therapy. Experimental biomarkers (i.e. non-approved biomarkers where the sensitivity (true positive rate/proportion of positives that are correctly identified) and/or specificity (true negative rate) are not as yet clear) are currently in development. These include approaches that estimate the presence/absence of an HRR defect via the identification of DNA mutations in BRCAness genes that control tumor cell responses to PARPi, approaches that estimate an HRR defect by identifying the extent and type of chromosomal alterations often found in BRCA mutant and BRCAness tumors and also functional biomarkers that use the visualization of key proteins involved in HRR as a predictor of the ability to repair PARPi-induced DNA lesions. (B) Clinical assessment of PARPi synthetic lethality. Most clinical trials assessing PARPi synthetic lethality have focused on tumor types that exhibit significant fractions of either germ-line BRCA1 or BRCA2 mutations or other candidate BRCAness defects. Regulatory bodies including the FDA and EMA have recently approved PARPi to be used in ovarian cancer patients with either BRCA1 or BRCA2 mutations (as shown) with these being detected via companion diagnostic assays.