Patricia F. Fitzpatrick Dimond Ph.D. Technical Editor of Clinical OMICs President of BioInsight Communications

Exploiting synthetic lethality for cancer therapy.

Drug candidate inhibitors of poly (ADP-ribose) polymerase 1 (PARP1) have generated interest among pharma companies and investors. But the enthusiasm waned when the PARP inhibitor iniparib, deemed “the next big thing” in cancer drug development, failed a Phase III clinical trial.

Despite the clinical failure of this PARP inhibitor, the basic science behind its development provides insights into the potential for exploiting “synthetic lethality” for cancer treatment, which takes place when either of two mutations occurring in a cell may have no effect on cell viability by itself, but the combination of the two mutations results in cell death.

The presence of one of these mutations in cancer cells, but not in normal cells, creates opportunities to selectively kill cancer cells by mimicking the effect of the second genetic mutation with targeted therapy, as in the case of PARP inhibitors. 

PARP enzymes play key roles in a form of DNA repair known as break excision repair, which fixes errors in one strand of DNA. PARP1 facilitates DNA repair by binding to DNA breaks and attracting DNA repair proteins to the damage site.

If a cell’s backup repair system is nonfunctional, however, as in the case of cancer cells carrying BRCA1 (tumor suppressor) and BRCA2 (DNA repair gene) mutations, the cell loses the ability to fix itself by homologous recombination. BRCA-related tumors thus must fall back on other ways to repair their DNA. If both BRCA and PARP mechanisms are dysfunctional, the cell dies. Therefore, investigators reasoned, tumors of patients carrying BRCA mutations could potentially be eliminated with chemical PARP inhibitors.

Commenting on the potential of exploiting this mechanism for novel cancer drugs, Daniel Silver, M.D., Ph.D., of Dana-Farber's Breast Oncology Center, said “This could be a very elegant way to utilize a defect in DNA repair without inflicting the same amount of damage to normal cells, because normal cells aren't defective in this compensating repair pathway.”


Validating Studies

Among the preclinical trials validating the pursuit of this class of compounds as potential anticancer agents was a 2005 study linking PARP activity to BRCA1 and BRCA2 mutations. Hannah Farmer, of the Cancer Research U.K. Gene Function and Regulation Group and The Breakthrough Breast Cancer Research Centre Institute of Cancer Research in London, and colleagues showed that BRCA1 or BRCA2 dysfunction profoundly sensitizes cells to the inhibition of PARP enzymatic activity, resulting in chromosomal instability, cell cycle arrest, and subsequent apoptosis.

According to the scientists, these results occurred because PARP inhibition leads to the persistence of DNA lesions normally repaired by homologous recombination. Their results illustrated, they said, how different pathways cooperate to repair damage, and suggest that the targeted inhibition of particular DNA repair pathways may allow the design of specific and less toxic therapies for cancer.

Buoyed by the potential anticancer properties of this new drug class, drug developers forged ahead with clinical studies of their small molecule PARP inhibitor candidates. But in January 2011, Sanofi announced that its small molecule oral PARP inhibitor iniparib had failed a Phase III study in women with triple-negative breast cancer. Earlier studies had suggested that the PARP inhibitor could extend progression-free survival when administered in a regimen that included gemcitabine and carboplatin.

When iniparib failed to help lung cancer patients in a late-stage trial, Sanofi reported in June 2013 that it had ended its research into the compound and took a $285 million charge. “In the case of iniparib, there may be an active drug in there somewhere, but at the moment there is no clear path for development,” said Chris Vienbacher, former Sanofi CEO.

Last June 25, FDA’s Oncologic Drugs Advisory Committee (ODAC) voted 11–2 to recommend that the agency postpone a decision on approving another PARP inhibitor, olaparib from AstraZeneca, until the company could present results in 2015 from the Phase III SOLO-2 trial testing the drug in treating BRAC mutated ovarian cancers. The drug was not approved after questions were raised about its potential side-effects as well as on the efficacy data demonstrating an improvement on progression-free survival.

While many clinical scientists would argue that the failed trials speak to poor trial design, others say the larger issue reflects a poor understanding of the basic science of how the drugs work, or in the case of iniparib, mistaken identity, as the drug candidate, it turns out, does not inhibit PARP.


More Research Needed

Aside from PARP1 and PARP2, which are both involved in the response to DNA damage, the functions of many of the other 17 currently recognized members of this protein family remain incompletely understood. Both PARP1 and PARP2 are inhibited by compounds in development. Multiple cancer types overexpress these enzymes but scientists note that the effect of these compounds on other PARP proteins remains unknown.

Data from in vitro experiments suggest that iniparib is not only structurally distinct from other described PARP inhibitors, but is also a poor inhibitor of PARP activity. Attempts to more fully characterize these proteins and how they differ from one another are ongoing.

The Mayo Clinic’s Scott Kaufmann, M.D., Ph.D., undertook preclinical studies comparing iniparib with the actions of the more extensively characterized PARP inhibitors olaparib and veliparib. He and his collaborators tested iniparib on cancer cells looking for signs of PARP inhibition in homologous recombination (HR)- deficient cell lines.

Their results, published in 2012 along with work from other groups, indicated that iniparib may not be a potent PARP inhibitor after all. The investigators compared the abilities of iniparib, olaparib, and veliparib to selectively induce apoptosis or inhibit colony formation in HR-deficient cell lines, selectively sensitize HR-proficient cells to topoisomerase I poisons, and inhibit formation of poly(ADP-ribose) polymer (pADPr) in intact cells.

As was the case with earlier-generation PARP inhibitors, olaparib and veliparib sensitized cells to camptothecin and topotecan, both topoisomerase I poisons and inhibited formation of pADPr in intact cells.

In further experiments, iniparib also failed to sensitize cells to cisplatin, gemcitabine, or paclitaxel.
While iniparib kills normal and neoplastic cells at high (>40 μmol/L) concentrations, the investigators concluded that its effects were “unlikely to reflect PARP inhibition and should not be used to guide decisions about other PARP inhibitors.

Abbott Laboratories’ Xuesong Liu, Ph.D., and colleagues reported that iniparib nonselectively modifies cysteine-containing proteins in tumor cells, and the primary mechanism of action for iniparib, as characterized in enzymatic, cellular, and in vivo assays, does not occur via inhibition of PARP activity.


Still in the Dark

The recent clinical failure of olaparib further begs the question of what PARP inhibitors really are and how drugs in development differ from one another. Dr. Kaufman noted that one potentially important long-term effect of PARP inhibition that has not been widely discussed is that PARP1 may function as a tumor-suppressor protein in cells, conceivably increasing the risk of secondary malignancies, particularly when PARP inhibitors are combined with genotoxic agents such as platins or topoisomerase I inhibitors.

Studies by National Cancer Institute (NCI) scientists further underscored that the mechanism of action of PARP inhibitors with regard to their effects in cancer cells is not fully understood. These investigations showed that PARP inhibitors not only attract PARP1 and PARP2 enzymes at damaged DNA, but trap them. Trapped PARP-DNA complexes proved more cytotoxic than unrepaired DNA single-strand breaks caused by PARP inactivation, arguing, the scientists said, that PARP inhibitors act in part as poisons that trap PARP enzyme on DNA. They also found that the potency in trapping PARP differed markedly among inhibitors with niraparib (MK-4827) > olaparib (AZD-2281) >> veliparib (ABT-888), a pattern not correlated with the catalytic inhibitory properties for each drug.

These findings suggested to the researchers that there may be two classes of PARP inhibitors, catalytic inhibitors that act mainly to inhibit PARP enzyme activity and do not trap PARP proteins on DNA, and dual inhibitors that both block PARP enzyme activity and act as PARP poison.

Despite mechanistic uncertainties, several PARP inhibitors remain in clinical trials. These include Lynparza (Olaparib, AZD-2281), Clovis Oncology’s Rucaparib (AG014699, PF-01367338) for metastatic breast and ovarian cancer, AbbVie’s Velaparib (ABT-888) in Phase III studies for metastatic melanoma and breast cancer, Cephalon’s CEP 9722 for non–small-cell lung cancer and Tesaro’s Phase niraparib, in Phase III for ovarian cancer.

NCI’s Junko Murai, M.D., Ph.D., sounded a cautionary note in a newsletter from the NCI. He said that his study results, in line with Dr. Kaufmann’s group, “Suggest that clinicians who use PARP inhibitors in clinical trials should carefully choose their drug, because we now suspect results may differ, depending upon the PARP inhibitor used. “As a next step, we are working to categorize other leading PARP inhibitors based upon both PARP trapping and PARP inhibition.”







































Patricia Fitzpatrick Dimond, Ph.D. (pdimond@genengnews.com), is technical editor at Genetic Engineering & Biotechnology News.