Current Molecular Pharmacology - Volume 5, Issue 1, 2012

The overall prognosis for advanced cancer remains poor. Although chemotherapy, radiotherapy and targeted agents have significantly improved patient outcomes, treatment related toxicity and the emergence of resistance negatively impact on survival. The therapeutic efficacy of many chemotherapeutic agents and ionising radiation is determined by their ability to induce DNA damage in cells. However, the DNA repair capacity of cancer cells to repair DNA damage induced by cytotoxic agents may directly influence treatment efficacy and resistance. Therefore, pharmacological inhibition of DNA repair in cancer cells has the potential to influence tumour response and clinical benefit to patients [1, 2]. The potential of DNA repair inhibitors has been confirmed in preclinical and clinical studies using Poly(ADP-ribose) polymerase (PARP) inhibitors [3-8]. PARPs are involved in the regulation of several cellular pathways including DNA base excision repair (BER) [9]. Tumours that are deficient in homologous recombination (HR) DNA repair pathway (tumours in patients with germline mutations in the BRCA1 or BRCA2 genes) are dependent upon other DNA repair pathways such as BER for survival. However therapeutic inhibition of BER using PARP inhibitors leads to the selective killing of BRCA1 or BRCA-2 tumour cell in the absence of any cytotoxic agent. The ability of PARP inhibitors to induce synthetic lethality in BRCA deficient breast and ovarian cancer suggests that other factors within BER are also potential synthetic lethality targets. Moreover, the ability of BER modulation to enhance cytotoxicity of alkylating agents and ionising radiation provides further evidence that BER factors are also likely to be promising targets to enhance therapeutic efficacy of anti-cancer agents. This exciting hot topic issue in Current Molecular Pharmaoclogy has brought together leading experts in the field to review the current status of BER in cancer therapy. As several reviews have been published recently on PARP inhibitors [5-8] we have decided to focus on BER targets other than PARP in this issue. Yun-Jeong Kim and David M.Wilson III have set the scene with an overview of BER biochemistry. BER pathway is complex and is usually initiated by a damage specific DNA glycosylase, which removes the damaged base creating an abasic site (apurinic/apyrimidinic, AP site). AP endonuclease (APE1) then cleaves the phosphodiester bond 5' to the AP site thereby generating a nick with 5'-sugar phosphate (dRP) and 3'-hydroxyl group. Members of the poly (ADP-ribose) polymerase (PARP) family of proteins get activated by single strand DNA breaks induced by APE1 and catalyse the addition of poly (ADP-ribose) polymers to target proteins, affecting protein-protein interactions. DNA polymerase β adds the first nucleotide to the 3'-end of the incised AP site. Normally, the reaction continues through the short-patch repair pathway where Pol β removes the 5'-sugar phosphate residue (by the process of β-elimination) and DNA ligase III-XRCC1 heterodimer (or DNA ligase I) then completes the repair [10-17]. AP sites are obligatory intermediates in the pathway for repair of alkylated bases (caused by alkylating agents such as temozolomide) and oxidised DNA bases (caused by ionising radiation) [18]. Unrepaired AP sites are cytotoxic and affect genomic integrity. In BER, AP sites are processed by AP endonucleases (APE1). APE1 is a multifunctional protein. The DNA repair function is performed by the C-terminal domain whereas the N-terminal domain is involved in redox regulation of transcription factors. Emerging preclinical and clinical data confirm that both C-terminal and N-terminal domains of APE1 are promising new drug targets. Odde et al. have reviewed the current status of APE1 DNA repair domain inhibitors in preclinical development. Kelley and co-workers have summarised the translational application of APE1 redox domain inhibitors in cancer. DNA polymerase β is also a promising drug target in BER. The biological relevance of Pol β and translesional synthesis is discussed by Nocolay et al. Strategies to impair Pol β function in cancer therapy have been β reviewed in detail by Goellner et al. It is increasingly clear that control of redox homeostasis impacts upon oxidative base damage. Storr and co-workers discuss the interesting links between DNA repair and redox regulation and applications to cancer therapy. Temozolomide is an important alkylating agent used in cancer therapy. The mechanisms of action of temozolomide, resistance mechanisms and strategies to bypass such resistance that impair therapeutic efficacy are discussed by Zhang et al. The narrow therapeutic index and the heterogeneity of patient responses to chemotherapy and radiotherapy imply that the efficacy of these agents could potentially be tailored based on tumour biology using predictive biomarkers. Gossage et al. provide the clinical evidence to support the view that BER factors are promising prognostic and predictive markers in cancer and could influence personalised cancer therapy in the future. In conclusion, this hot topic issue is the first comprehensive summary of emerging drug targets in BER and will provide essential information for basic scientists, pharmaceutical scientists and clinicians interested in cancer therapy. DNA repair is the next new frontier in anti-cancer discovery. A concerted collaborative effort by the pharmaceutical industry and academic research groups will help accelerate drug development targeting DNA repair in the near future.

Base excision repair (BER) is an evolutionarily conserved pathway, which could be considered the “workhorse” repair mechanism of the cell. In particular, BER corrects most forms of spontaneous hydrolytic decay products in DNA, as well as everyday oxidative and alkylative modifications to bases or the sugar phosphate backbone. The repair response involves five key enzymatic steps that aim to remove the initial DNA lesion and restore the genetic material back to its original state: (i) excision of a damaged or inappropriate base, (ii) incision of the phosphodiester backbone at the resulting abasic site, (iii) termini clean-up to permit unabated repair synthesis and/or nick ligation, (iv) gap-filling to replace the excised nucleotide, and (v) sealing of the final, remaining DNA nick. These repair steps are executed by a collection of enzymes that include DNA glycosylases, apurinic/apyrimidinic endonucleases, phosphatases, phosphodiesterases, kinases, polymerases and ligases. Defects in BER components lead to reduced cell survival, elevated mutation rates, and DNA-damaging agent hypersensitivities. In addition, the pathway plays a significant role in determining cellular responsiveness to relevant clinical anti-cancer agents, such as alkylators (e.g. temozolomide), nucleoside analogs (e.g. 5-fluorouracil), and ionizing radiation. The molecular details of BER and the contribution of the pathway to therapeutic agent resistance are reviewed herein.

APE1 is a multifaceted protein that orchestrates multiple activities in the cell, one of which is the preservation of genomic integrity; a vital process that takes place in the context of the base excision repair (BER) pathway. Studies have implicated APE1 in rendering cancerous cells less vulnerable to the effects of DNA-damaging agents that are commonly used for the treatment of cancer. Furthermore, suppression of APE1 expression in cancer cell lines is accompanied by the potentiation of the activity of cytotoxic agents. As a result, major efforts have been directed towards the identification of small-molecule inhibitors of this DNA-repair enzyme. Herein, we review all patented small-molecule APE1 inhibitors reported prior to 2011. Unfortunately, the potency and selectivity of many of the reported inhibitors were not disclosed by the original authors, and at present it is unclear if APE1 is a bona fide target for many of the purported inhibitors. Moreover, cellular activity and toxicity of many inhibitors remain to be established. Since this is the first comprehensive review of small molecule APE1 inhibitors, we present all compounds reported to inhibit APE1 activity with an IC50 value ≤ 25 μM. Efforts towards a careful validation and optimization of these compounds are warranted. Furthermore, we explore potential allosteric drug-binding sites on the protein as an alternative approach for modulating the activity of this multifunctional protein. In addition, we give an overview of APE2, as well as other APE1 homologues in some disease-causing pathogens. Finally, given the universal importance of DNA repair, as well as the considerable conservation of repair proteins across all living organisms, we propose targeting the AP endonuclease activity of pathogens by the compounds discussed in this review, thereby expanding their therapeutic potential and application.

The heterogeneity of most cancers diminishes the treatment effectiveness of many cancer-killing regimens. Thus, treatments that hold the most promise are ones that block multiple signaling pathways essential to cancer survival. One of the most promising proteins in that regard is APE1, whose reduction-oxidation activity influences multiple cancer survival mechanisms, including growth, proliferation, metastasis, angiogenesis, and stress responses. With the continued research using APE1 redox specific inhibitors alone or coupled with developing APE1 DNA repair inhibitors it will now be possible to further delineate the role of APE1 redox, repair and protein-protein interactions. Previously, use of siRNA or over expression approaches, while valuable, do not give a clear picture of the two major functions of APE1 since both techniques severely alter the cellular milieu. Additionally, use of the redox-specific APE1 inhibitor, APX3330, now makes it possible to study how inhibition of APE1's redox signaling can affect multiple tumor pathways and can potentiate the effectiveness of existing cancer regimens. Because APE1 is an upstream effector of VEGF, as well as other molecules that relate to angiogenesis and the tumor microenvironment, it is also being studied as a possible treatment for agerelated macular degeneration and diabetic retinopathy. This paper reviews all of APE1's functions, while heavily focusing on its redox activities. It also discusses APE1's altered expression in many cancers and the therapeutic potential of selective inhibition of redox regulation, which is the subject of intense preclinical studies.

The cellular genome is constantly subject to DNA damage caused by endogenous factors or exogenously by damaging agents such as ionizing radiation or various anticancer agents. The base excision repair (BER) enzyme, DNA polymerase β, and the polymerases involved in translesion synthesis (TLS) have been shown to contribute to cellular tolerance and repair of DNA lesions by anticancer treatments, particularly the platinum cytotoxic drugs. Moreover, there is robust preclinical evidence linking alterations in DNA pol β and TLS polymerase levels to cancer. DNA polymerases may therefore be potential targets to increase the sensitivity of cancer cells to chemotherapy drugs. In this article, the physical and chemical properties of DNA polymerase β and the translesion synthesis polymerases are reviewed with a view to identifying how they may act as targets for anticancer treatment. The potential clinical role of new DNA polymerase inhibitors is discussed and how they may be combined with conventional cytotoxic agents.

DNA damage plays a causal role in numerous disease processes. Hence, it is suggested that DNA repair proteins, which maintain the integrity of the nuclear and mitochondrial genomes, play a critical role in reducing the onset of multiple diseases, including cancer, diabetes and neurodegeneration. As the primary DNA polymerase involved in base excision repair, DNA polymerase ß (Polß) has been implicated in multiple cellular processes, including genome maintenance and telomere processing and is suggested to play a role in oncogenic transformation, cell viability following stress and the cellular response to radiation, chemotherapy and environmental genotoxicants. Therefore, Polß inhibitors may prove to be effective in cancer treatment. However, Polß has a complex and highly regulated role in DNA metabolism. This complicates the development of effective Polß-specific inhibitors useful for improving chemotherapy and radiation response without impacting normal cellular function. With multiple enzymatic activities, numerous binding partners and complex modes of regulation from post-translational modifications, there are many opportunities for Polß inhibition that have yet to be resolved. To shed light on the varying possibilities and approaches of targeting Polß for potential therapeutic intervention, we summarize the reported small molecule inhibitors of Polß and discuss the genetic, biochemical and chemical studies that implicate additional options for Polß inhibition. Further, we offer suggestions on possible inhibitor combinatorial approaches and the potential for tumor specificity for Polß-inhibitors.

Control of redox homeostasis is crucial for a number of cellular processes with deregulation leading to a number of serious consequences including oxidative damage such induction of DNA base lesions. The DNA lesions caused by oxidative damage are principally repaired by the base excision repair (BER) pathway. Pharmacological inhibition of BER is becoming an increasingly active area of research with the emergence of PARP inhibitors in cancer therapy. The redox status of the cell is modulated by a number of systems, including a large number of anti-oxidant enzymes who function in the control of superoxide and hydrogen peroxide, and ultimately in the release of the damaging hydroxyl radical. Here we provide an overview of reactive oxygen species (ROS) production and its modulation by antioxidant enzymes. The review also discusses the effect of ROS on the BER pathway, particularly in relation to cancer. Finally, as the modulation of the redox environment is of interest in cancer therapy, with certain agents having the potential to reverse chemo- and radiotherapy resistance or treat therapy related toxicity, we discuss redox modulating agents currently under development.

Glioblastoma multiforme is the most common aggressive adult primary tumour of the central nervous system. Treatment includes surgery, radiotherapy and adjuvant temozolomide (TMZ) chemotherapy. TMZ is an alkylating agent prodrug, delivering a methyl group to purine bases of DNA (O6-guanine; N7-guanine and N3-adenine). The primary cytotoxic lesion, O6-methylguanine (O6-MeG) can be removed by methylguanine methyltransferase (MGMT; direct repair) in tumours expressing this protein, or tolerated in mismatch repair-deficient (MMR-) tumours. Thus MGMT or MMR deficiency confers resistance to TMZ. Inherent- and acquired resistance to TMZ present major obstacles to successful treatment. Strategies devised to thwart resistance and enhance response to TMZ, including inhibition of DNA repair mechanisms which contribute to TMZ resistance, are under clinical evaluation. Depletion of MGMT prior to alkylating agent chemotherapy prevents O6-MeG repair; thus, MGMT pseudosubstrates O6-benzylguanine and lomeguatrib are able to sensitise tumours to TMZ. Disruption of base excision repair (BER) results in persistence of potentially lethal N7- and N3- purine lesions contributing significantly to TMZ cytoxicity particularly when O6-MeG adducts are repaired or tolerated. Several small molecule inhibitors of poly(ADP-ribose)polymerase-1 (PARP-1), a critical BER protein are yielding promising results clinically, both in combination with TMZ and as single agent chemotherapy in patients whose tumours possess homologous recombination DNA repair defects. Another validated, but as yet preclinical protein target, mandatory to BER is abasic (AP) endonuclease-1 (APE-1); in preclinical tests, APE-1 inhibition potentiates TMZ activity. An alternative strategy is synthesis of a molecule, evoking an irrepairable cytotoxic O6-G lesion. Preliminary efforts to achieve this goal are described.

The cytotoxicity of both chemotherapy and radiotherapy is to a large extent directly related to their ability to induce DNA damage. The ability of cancer cells to recognise and repair this damage contributes to therapeutic resistance. Sub-optimal DNA repair in normal tissue may impair normal tissue tolerance. Inter-individual differences in DNA repair pathways may also influence the natural history and progression of cancer and hence prognosis. The base excision repair (BER) pathway has evolved to repair base damage induced by endogenous and exogenous base targeting agents. Polymorphic variants of genes, mRNA expression and alterations in protein expression within BER, may alter DNA repair capacity and influence both cancer progression and clinical responses to chemotherapy and radiotherapy. We discuss the role of BER genes as potential predictive and prognostic markers in human cancer and review the current state of play within this field.