DNA Religation Research Articles

Programmed activation of cancer cell apoptosis: A tumor-targeted phototherapeutic topoisomerase I inhibitor.

We report here a tumor-targeting masked phototherapeutic agent 1 (PT-1). This system contains SN-38—a prodrug of the topoisomerase I inhibitor irinotecan. Topoisomerase I is a vital enzyme that controls DNA topology during replication, transcription, and recombination. An elevated level of topoisomerase I is found in many carcinomas, making it an attractive target for the development of effective anticancer drugs. In addition, PT-1 contains both a photo-triggered moiety (nitrovanillin) and a cancer targeting unit (biotin). Upon light activation in cancer cells, PT-1 interferes with DNA re-ligation, diminishes the expression of topoisomerase I, and enhances the expression of inter alia mitochondrial apoptotic genes, death receptors, and caspase enzymes, inducing DNA damage and eventually leading to apoptosis. In vitro and in vivo studies showed significant inhibition of cancer growth and the hybrid system PT-1 thus shows promise as a programmed photo-therapeutic (“phototheranostic”).

Coordinated Dynamics Orchestrating the DNA Re-Ligation by De-Poisoned Topoisomerase II

Topoisomerase II is a crucial enzyme that tightly controls the topology of DNA to facilitate the critical sub-cellular processes involving these genetic materials. It generates transient double-strand breaks (DSB) and transports another DNA duplex through to resolve their topological problems. Although topoisomerase poisons, the drugs arresting the subsequent DNA re-ligation, have been used in anticancer therapy and the recent structural characterization of the enzyme, our understanding of the re-ligation mechanism was still distressingly restricted by the transitory nature of this process. Captivated by the fluent re-ligation following the characteristic DSB by the enzyme, we selected a high-resolution crystal structure of the drug-entrapped intermediate and exploited atomistic molecular dynamics simulations of the very large systems for up to a microsecond to investigate the dynamics of this process [1]. We observed a nearly vectorial transition of the de-poisoned complex toward the resealing-compliant configuration, and the statistical analysis revealed the non-concerted maneuvers of the two different DNA strands mediated by the enzyme. Using a neighborhood-based metric, we captured the important dynamical transitions during the re-ligation from the vast amount of correlated motions and provided the visible links between previously unsettled experimental observations. With the simulations of the drug-bound complexes, we also presented the conformational population shifts of an important residue in response to the binding of different drug molecules [2]. Furthermore, by comparing the coordinated dynamics revealed by different isoforms, we are able to dissect the differential dynamics of the critical DNA re-ligation conducted by the enzymes. We believe these are useful insights for the development of new anticancer drugs with lower cardiotoxicity.

Processing of Nonconjugative Resistance Plasmids by Conjugation Nicking Enzyme of Staphylococci.

Antimicrobial resistance in Staphylococcus aureus presents an increasing threat to human health. This resistance is often encoded on mobile plasmids, such as pSK41; however, the mechanism of transfer of these plasmids is not well understood. In this study, we first examine key protein-DNA interactions formed by the relaxase enzyme, NES, which initiates and terminates the transfer of the multidrug resistance plasmid pSK41. Two loops on the NES protein, hairpin loops 1 and 2, form extensive contacts with the DNA hairpin formed at the oriT region of pSK41, and here we establish that these contacts are essential for proper DNA cleavage and religation by the full 665-residue NES protein in vitro. Second, pSK156 and pCA347 are nonconjugative Staphylococcus aureus plasmids that contain sequences similar to the oriT region of pSK41 but differ in the sequence predicted to form a DNA hairpin. We show that pSK41-encoded NES is able to bind, cleave, and religate the oriT sequences of these nonconjugative plasmids in vitro. Although pSK41 could mobilize a coresident plasmid harboring its cognate oriT, it was unable to mobilize plasmids containing the pSK156 and pCA347 variant oriT mimics, suggesting that an accessory protein like that previously shown to confer specificity in the pWBG749 system may also be involved in transmission of plasmids containing a pSK41-like oriT. These data indicate that the conjugative relaxase in trans mechanism recently described for the pWBG749 family of plasmids also applies to the pSK41 family of plasmids, further heightening the potential significance of this mechanism in the horizontal transfer of staphylococcal plasmids. Understanding the mechanism of antimicrobial resistance transfer in bacteria such as Staphylococcus aureus is an important step toward potentially slowing the spread of antimicrobial-resistant infections. This work establishes protein-DNA interactions essential for the transfer of the Staphylococcus aureus multiresistance plasmid pSK41 by its relaxase, NES. This enzyme also processed variant oriT-like sequences found on numerous plasmids previously considered nontransmissible, suggesting that in conjunction with an uncharacterized accessory protein, these plasmids may be transferred horizontally via a relaxase in trans mechanism. These findings have important implications for our understanding of staphylococcal resistance plasmid evolution.

The dual topoisomerase inhibitor A35 preferentially and specially targets topoisomerase 2α by enhancing pre-strand and post-strand cleavage and inhibiting DNA religation.

DNA topoisomerases play a key role in tumor proliferation. Chemotherapeutics targeting topoisomerases have been widely used in clinical oncology, but resistance and side effects, particularly cardiotoxicity, usually limit their application. Clinical data show that a decrease in topoisomerase (top) levels is the primary factor responsible for resistance, but in cells there is compensatory effect between the levels of top1 and top2α. Here, we validated cyclizing-berberine A35, which is a dual top inhibitor and preferentially targets top2α. The impact on the top2α catalytic cycle indicated that A35 could intercalate into DNA but did not interfere with DNA-top binding and top2α ATPase activity. A35 could facilitate DNA-top2α cleavage complex formation by enhancing pre-strand and post-strand cleavage and inhibiting religation, suggesting this compound can be a topoisomerase poison and had a district mechanism from other topoisomerase inhibitors. TARDIS and comet assays showed that A35 could induce cell DNA breakage and DNA-top complexes but had no effect on the cardiac toxicity inducer top2β. Silencing top1 augmented DNA break and silencing top2α decreased DNA break. Further validation in H9c2 cardiac cells showed A35 did not disturb cell proliferation and mitochondrial membrane potency. Additionally, an assay with nude mice further demonstrated A35 did not damage the heart. Our work identifies A35 as a novel skeleton compound dually inhibits topoisomerases, and predominantly and specially targets top2α by interfering with all cleavage steps and its no cardiac toxicity was verified by cardiac cells and mice heart. A35 could be a novel and effective targeting topoisomerase agent.

Redesign of the monomer-monomer interface of Cre recombinase yields an obligate heterotetrameric complex.

Cre recombinase catalyzes the cleavage and religation of DNA at loxP sites. The enzyme is a homotetramer in its functional state, and the symmetry of the protein complex enforces a pseudo-palindromic symmetry upon the loxP sequence. The Cre-lox system is a powerful tool for many researchers. However, broader application of the system is limited by the fixed sequence preferences of Cre, which are determined by both the direct DNA contacts and the homotetrameric arrangement of the Cre monomers. As a first step toward achieving recombination at arbitrary asymmetric target sites, we have broken the symmetry of the Cre tetramer assembly. Using a combination of computational and rational protein design, we have engineered an alternative interface between Cre monomers that is functional yet incompatible with the wild-type interface. Wild-type and engineered interface halves can be mixed to create two distinct Cre mutants, neither of which are functional in isolation, but which can form an active heterotetramer when combined. When these distinct mutants possess different DNA specificities, control over complex assembly directly discourages recombination at unwanted half-site combinations, enhancing the specificity of asymmetric site recombination. The engineered Cre mutants exhibit this assembly pattern in a variety of contexts, including mammalian cells.

Recovery of the poisoned topoisomerase II for DNA religation: coordinated motion of the cleavage core revealed with the microsecond atomistic simulation.

Type II topoisomerases resolve topological problems of DNA double helices by passing one duplex through the reversible double-stranded break they generated on another duplex. Despite the wealth of information in the cleaving operation, molecular understanding of the enzymatic DNA ligation remains elusive. Topoisomerase poisons are widely used in anti-cancer and anti-bacterial therapy and have been employed to entrap the intermediates of topoisomerase IIβ with religatable DNA substrate. We removed drug molecules from the structure and conducted molecular dynamics simulations to investigate the enzyme-mediated DNA religation. The drug-unbound intermediate displayed transitions toward the resealing-compliant configuration: closing distance between the cleaved DNA termini, B-to-A transformation of the double helix, and restoration of the metal-binding motif. By mapping the contact configurations and the correlated motions between enzyme and DNA, we identified the indispensable role of the linker preceding winged helix domain (WHD) in coordinating the movements of TOPRIM, the nucleotide-binding motifs, and the bound DNA substrate during gate closure. We observed a nearly vectorial transition in the recovery of the enzyme and identified the previously uncharacterized roles of Asn508 and Arg677 in DNA rejoining. Our findings delineate the dynamic mechanism of the DNA religation conducted by type II topoisomerases.

Repair synthesis step involving ERCC1-XPF participates in DNA repair of the Top1-DNA damage complex.

Topoisomerase 1 (Top1) is the intercellular target of camptothecins (CPTs). CPT blocks DNA religation in the Top1-DNA complex and induces Top1-attached nick DNA lesions. In this study, we demonstrate that excision repair cross complementing 1 protein-xeroderma pigmentosum group F (ERCC1-XPF) endonuclease and replication protein A (RPA) participate in the repair of Top1-attached nick DNA lesions together with other nucleotide excision repair (NER) factors. ERCC1-XPF shows nuclease activity in the presence of RPA on a 3'-phosphotyrosyl bond nick-containing DNA (Tyr-nick DNA) substrate, which mimics a Top1-attached nick DNA lesion. In addition, ERCC1-XPF and RPA form a DNA/protein complex on the nick DNA substrate in vitro, and co-localize in CPT-treated cells in vivo. Moreover, the DNA repair synthesis of Tyr-nick DNA lesions occurred in the presence of NER factors, including ERCC1-XPF, RPA, DNA polymerase delta, flap endonuclease 1 and DNA ligase 1. Therefore, some of the NER repair machinery might be an alternative repair pathway for Top1-attached nick DNA lesions. Clinically, these data provide insights into the potential of ERCC1 as a biomarker during CPT regimens.

The distinctive cellular responses to DNA strand breaks caused by a DNA topoisomerase I poison in conjunction with DNA replication and RNA transcription.

Camptothecin (CPT) inhibits DNA topoisomerase I (Top1) through a non-catalytic mechanism that stabilizes the Top1-DNA cleavage complex (Top1cc) and blocks the DNA re-ligation step, resulting in the accumulation in the genome of DNA single-strand breaks (SSBs), which are converted to secondary strand breaks when they collide with the DNA replication and RNA transcription machinery. DNA strand breaks mediated by replication, which have one DNA end, are distinct in repair from the DNA double-strand breaks (DSBs) that have two ends and are caused by ionizing radiation and other agents. In contrast to two-ended DSBs, such one-ended DSBs are preferentially repaired through the homologous recombination pathway. Conversely, the repair of one-ended DSBs by the non-homologous end-joining pathway is harmful for cells and leads to cell death. The choice of repair pathway has a crucial impact on cell fate and influences the efficacy of anticancer drugs such as CPT derivatives. In addition to replication-mediated one-ended DSBs, transcription also generates DNA strand breaks upon collision with the Top1cc. Some reports suggest that transcription-mediated DNA strand breaks correlate with neurodegenerative diseases. However, the details of the repair mechanisms of, and cellular responses to, transcription-mediated DNA strand breaks still remain unclear. In this review, combining our recent results and those of previous reports, we introduce and discuss the responses to CPT-induced DNA damage mediated by DNA replication and RNA transcription.

Novel DNA topoisomerase IIα inhibitors from combined ligand- and structure-based virtual screening.

DNA topoisomerases are enzymes responsible for the relaxation of DNA torsional strain, as well as for the untangling of DNA duplexes after replication, and are important cancer drug targets. One class of topoisomerase inhibitors, “poisons”, binds to the transient enzyme-DNA complex which occurs during the mechanism of action, and inhibits the religation of DNA. This ultimately leads to the accumulation of DNA double strand breaks and cell death. Different types of topoisomerases occur in human cells and several poisons of topoisomerase I and II are widely used clinically. However, their use is compromised by a variety of side effects. Recent studies confirm that the inhibition of the α-isoform of topoisomerase II is responsible for the cytotoxic effect, whereas the inhibition of the β-isoform leads to development of adverse drug reactions. Thus, the discovery of agents selective for topoisomerase IIα is an important strategy for the development of topoisomerase II poisons with improved clinical profiles. Here, we present a computer-aided drug design study leading to the identification of structurally novel topoisomerase IIα poisons. The study combines ligand- and structure-based drug design methods including pharmacophore models, homology modelling, docking, and virtual screening of the National Cancer Institute compound database. From the 8 compounds identified from the computational work, 6 were tested for their capacity to poison topoisomerase II in vitro: 4 showed selective inhibitory activity for the α- over the β-isoform and 3 of these exhibited cytotoxic activity. Thus, our study confirms the applicability of computer-aided methods for the discovery of novel topoisomerase II poisons, and presents compounds which could be investigated further as selective topoisomerase IIα inhibitors.

Potent Inhibition of the Growth and Induction of Apoptosis of Mantle Cell Lymphoma By the Novel Anthracycline Berubicin in Vitro and in Vivo

Rituximab in combination with hyperfractionated cyclophosphamide, vincristine, doxorubicin (DOX), and dexamethasone has been a successful frontline therapy for aggressive mantle cell lymphoma (MCL), a distinct and heterogeneous subtype of non-Hodgkin lymphoma, with complete remission rates as high as 87% in patients at or below 65 years of age. However, the efficacy of rituximab in combination with hyperfractionated cyclophosphamide, vincristine, DOX, and dexamethasone comes at the expense of severe grade III-IV toxic effects, and its use is limited by de novoor acquired multidrug resistance. Berubicin (WP744; BRN) is a clinically evaluated analog of DOX that, like DOX, stabilizes cleavable complexes between DNA and topoisomerase II, leading to irreversible double-strand DNA breaks and abrogation of DNA religation. In contrast to DOX, BRN overcomes multidrug resistance by circumventing efflux mediated by ATP-binding cassette proteins like P-glycoprotein and MRP-1. BRN is also the first anthracycline derivative to effectively cross the blood-brain barrier, with demonstrated phase 1 responses in brain cancer patients. Our MCL studies demonstrated that treatment with BRN decreased cell growth threefold to sixfold more potently than DOX in all tested MCL cell lines (Mino, Jeko-1, SP53, and Granta 519) and four MCL patient samples by arresting MCL cell-cycle progression at the G2/M phase and inducing extensive apoptosis. Moreover, in a Western blot assay, Jeko-1 and Mino cells exhibited activation of caspase-3 and caspase-9 and cleavage of poly(ADP-ribose) polymerase over time, pointing to the presence of a mitochondria-mediated apoptosis pathway in BRN-treated MCL cell lines. We then assessed the in vivo activity of BRN, using DOX as a control, in MCL-bearing severe combined immunodeficient (SCID) and SCID-hu mice. Our results indicated that SCID mice given 10 mg/kg DOX survived no more than 15 days after treatment, whereas all mice given 10 mg/kg BRN survived up to 63 days after treatment. On the other hand, when BRN and DOX were administered at lower doses of 5 mg/kg in a SCID-hu MCL mouse model, similar survival durations for BRN and DOX were observed. In summary, our studies demonstrate that BRN is highly potent against MCL in vitro and displays a wider therapeutic window than DOX, delivering very promising in vivo activity in both SCID and SCID-hu MCL models. These results indicate that BRN should be evaluated in the treatment of other lymphomas and seriously considered as an effective replacement for DOX in MCL treatment. BRN’s success in Phase 1 studies in glioma patients and observed safety and effectiveness in MCL models warrant further investigation of its clinical use and combination with existing therapies in MCL patients. DisclosuresPriebe:MD Anderson: Waldemar Priebe holds patents and has a financial interest in the development of berubicin. Patents & Royalties.

Inhibition of Mycobacterium tuberculosis topoisomerase I by m-AMSA, a eukaryotic type II topoisomerase poison

m-AMSA, an established inhibitor of eukaryotic type II topoisomerases, exerts its cidal effect by binding to the enzyme–DNA complex thus inhibiting the DNA religation step. The molecule and its analogues have been successfully used as chemotherapeutic agents against different forms of cancer. After virtual screening using a homology model of the Mycobacterium tuberculosis topoisomerase I, we identified m-AMSA as a high scoring hit. We demonstrate that m-AMSA can inhibit the DNA relaxation activity of topoisomerase I from M. tuberculosis and Mycobacterium smegmatis. In a whole cell assay, m-AMSA inhibited the growth of both the mycobacteria.

Abstract B87: Preclinical investigation of the potentiation in antitumor effect of TAS-102, a novel oral anti-neoplastic nucleoside agent, in combination with irinotecan (CPT-11) in colorectal cancer.

Abstract Background: Irinotecan (CPT-11) is a topoisomeraseI (TopoI) inhibitor, which is widely used for the treatment of metastatic colorectal cancer. CPT-11 inhibits DNA religation by TopoI, thus it stabilizes DNA-TopoI complexes and subsequently induces cytotoxicity. TAS-102, a novel oral antitumor agent, consisting of trifluorothymidine(FTD) and thymidine phosphorylase inhibitor, has reported promising clinical results in metastatic colorectal cancer. Several reports indicated that aberrant nucleoside incorporation into DNA, such as with cytarabine or gemcitabine, enhanced DNA-TopoI complexes. FTD, the effector of TAS-102, is a nucleoside which is efficiently incorporated and retained into DNA. Here, we evaluated the potency of TAS-102 in combination with CPT-11 in vitro and in vivo Materials and Methods: The combinational effect of FTD and SN-38 which is the active metabolite of CPT-11 was evaluated with several treatment schedules. Various colorectal cancer cell lines (SW48, SW620, LS174T and HCT116) were used in this assay. In one set, cells were washed after a 24 hour pre-exposure to FTD followed by a 48 hour exposure to SN-38 (FTD pre-exposure schedule); in the other set, cells were washed after a 6 hour pre-exposure to SN-38 followed by a 66 hour exposure to FTD (SN-38 pre-exposure schedule). A combinational intensity was estimated by using a combination index (CI) which indicates synergism (CI<0.8), additivity (0.8<CI<1.2), or antagonism (CI>1.2). Additionally, the antitumor effect of TAS-102 in combination with CPT-11 was investigated in a human colorectal cancer xenograft model. TAS-102 was orally administered for 14 days consecutively and CPT-11 was intravenously administered once a week to mice. Results: The combination of SN-38 and FTD showed a synergistic effect (SW48, SW620 and LS174T) or an additive effect (HCT116) in both the FTD pre-exposure schedule as well as the SN-38 pre-exposure schedule. Also, the enhancement of antitumor effect of TAS-102 in combination with CPT-11 was observed in vivo. Furthermore, these cell lines had various genotypes as regards KRAS, PI3CA and other DNA repair enzymes frequently detected in colorectal cancer, indicating that the combination's efficacy seemed to be independent of genetic status. Conclusion: TAS-102/CPT-11 represents a novel combination strategy for the treatment of advanced colorectal cancer. A synergistic effect was observed in both schedules tested, suggesting that various underlying mechanisms may exist. One potential mechanism is that FTD uptake or incorporation into DNA is increased by TopoI inhibition, and that FTD incorporation then further stabilizes the CPT-11 induced cleavable complex. However, the precise mechanism needs to be elucidated in the future. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B87. Citation Format: Keiji Ishida, Nozomu Tanaka, Sayaka Tsukioka, Kokoro Eshima, Akio Fujioka, Keisuke Yamamura, Satoko Ito, Kenichi Matsuo, Teruhiro Utsugi. Preclinical investigation of the potentiation in antitumor effect of TAS-102, a novel oral anti-neoplastic nucleoside agent, in combination with irinotecan (CPT-11) in colorectal cancer. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B87.

Dual topoisomerase I and II poisoning by chiral Ru(II) complexes containing 2-thiophenylimidazo[4,5-f][1,10]phenanthroline derivatives

A series of chiral Ru(II) complexes bearing thiophene ligands were synthesized and characterized. Both Ru(II) complexes Δ/Λ-[Ru(bpy)2(pscl)]2+ (Δ/Λ-1) and Δ/Λ-[Ru(bpy)2(psbr)]2+ (Δ/Λ-2) (bpy=2,2′-bipyridine, pscl=2-(5-chlorothiophen-2-yl)imidazo[4,5-f][1,10]phenanthroline, psbr=2-(5-bromothiophen-2-yl)imidazo[4,5-f][1,10]phenanthroline) showed antitumor activities against A549, HepG2 and BEL-7402 tumor cell lines, especially HeLa tumor cell line. Moreover, Δ enantiomers were more active than Λ enantiomers, accounting for the different cellular uptake. In addition, with the extension of time, these enantiomers could finally accumulate in the nucleus, suggesting that nucleic acids were the cellular target of these enantiomers. The DNA-binding behaviors of complexes were studied using spectroscopic and viscosity measurements. Results suggested that four complexes could bind to DNA in an intercalative mode but no obvious DNA-binding selectivity between the enantiomers was observed. Topoisomerase inhibition and DNA religation assay confirmed that four complexes acted as efficient dual topoisomerase I and II poisons, DNA strand breaks had also been observed from alkaline single cell gel electrophoresis (comet assay). Δ-1 and Δ-2 inhibited the growth of HeLa cells through the induction of apoptotic cell death, as evidenced by the Alexa Fluor® 488 annexin V staining assays and flow cytometry analysis. The results demonstrated that Δ/Λ-1 and Δ/Λ-2 acted as dual topoisomerase I and II poisons and caused DNA damage that could lead to cell cycle arrest by apoptosis.

Substrate-mediated proton relay mechanism for the religation reaction in topoisomerase II

The DNA religation reaction of yeast type II topoisomerase (topo II) was investigated to elucidate its metal-dependent general acid/base catalysis. Quantum mechanical/molecular mechanical calculations were performed for the topo II religation reaction, and the proton transfer pathway was examined. We found a substrate-mediated proton transfer of the topo II religation reaction, which involves the 3′ OH nucleophile, the reactive phosphate, water, Arg781, and Tyr782. Metal A stabilizes the transition states, which is consistent with a two-metal mechanism in topo II. This pathway may be required for the cleavage/religation reaction of topo IA and II and will provide a general explanation for the catalytic mechanism in the topo IA and II.

Carboxyl terminal domain basic amino acids of mycobacterial topoisomerase I bind DNA to promote strand passage

Bacterial DNA topoisomerase I (topoI) carries out relaxation of negatively supercoiled DNA through a series of orchestrated steps, DNA binding, cleavage, strand passage and religation. The N-terminal domain (NTD) of the type IA topoisomerases harbor DNA cleavage and religation activities, but the carboxyl terminal domain (CTD) is highly diverse. Most of these enzymes contain a varied number of Zn2+ finger motifs in the CTD. The Zn2+ finger motifs were found to be essential in Escherichia coli topoI but dispensable in the Thermotoga maritima enzyme. Although, the CTD of mycobacterial topoI lacks Zn2+ fingers, it is indispensable for the DNA relaxation activity of the enzyme. The divergent CTD harbors three stretches of basic amino acids needed for the strand passage step of the reaction as demonstrated by a new assay. We also show that the basic amino acids constitute an independent DNA-binding site apart from the NTD and assist the simultaneous binding of two molecules of DNA to the enzyme, as required during the catalytic step. Although the NTD binds to DNA in a site-specific fashion to carry out DNA cleavage and religation, the basic residues in CTD bind to non-scissile DNA in a sequence-independent manner to promote the crucial strand passage step during DNA relaxation. The loss of Zn2+ fingers from the mycobacterial topoI could be associated with Zn2+ export and homeostasis.

Abstract 3324: The discovery and optimisation of small-molecule inhibitors of human 5’-tyrosyl DNA phosphodiesterase (Tdp2).

Abstract Topoisomerases (topo) regulate DNA topology by the transient cleavage and re-ligation of DNA during transcription and replication. Topo II poisons such as etoposide can induce abortive DNA strand breaks in which topo II remains covalently bound to a 5’ DNA strand terminus via a phosphotyrosyl linker. Tyrosyl DNA phosphodiesterase 2 (Tdp2, TTRAP, EAPII) is a recently discovered human 5’-tyrosyl DNA phosphodiesterase which repairs this topo-mediated DNA damage, therefore playing a central role in maintaining normal DNA topology in cells. Cellular depletion of Tdp2 has been shown to result in an increased susceptibility and sensitivity to topo II-induced DNA double strand breaks. It has therefore been proposed that selective pharmacological inhibition of Tdp2 may be a novel approach to overcome intrinsic or acquired resistance to topo II targeted drug therapy. To date, no known drug-like inhibitors of Tdp2 have been identified. We have recently reported a robust ‘mix and read’ HTS compatible assay and this was used to screen a diverse chemical library of approximately 92,000 compounds. From this endeavour, 2 distinct hit series have been identified. Following further chemical exploration of the original hit compounds, small molecule inhibitors of Tdp2 with sub-100nM potencies have been identified. This poster will describe our biological and chemical progress in this area, detailing SAR and some lessons learnt during investigation of this target. Citation Format: Allan M. Jordan, Paul Depledge, Nicola Hamilton, James Hitchin, Gemma Hopkins, Laura Maguire, Alison McGonagle, Daniel Mould, Ali Raoof, Mathew Rushbrooke, James Smith, Kate Smilth, Graeme Thomson, Fabrice Turlais, Ian Waddell, Mandy Watson, Donald Ogilvie. The discovery and optimisation of small-molecule inhibitors of human 5’-tyrosyl DNA phosphodiesterase (Tdp2). [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3324. doi:10.1158/1538-7445.AM2013-3324

Abstract 4480: New approaches to changing an enzyme into a cytotoxic agent: A novel way to stimulate DNA cleavage by topoisomerase II.

Abstract Topoisomerase poisons are important anti-cancer drugs, and include agents such as etoposide and doxorubicin that target eukaryotic topoisomerase II. Most topoisomerase II poisons act as interstitial inhibitors. This mode of inhibition depends on the coordination of the enzyme and DNA substrate to form a drug binding site. While recent structural studies have localized topoisomerase II poisons to the drug/DNA interface, our understanding of the mechanism of enzyme inhibition remains incomplete. We have combined genetic, biochemical, and structural approaches to identify regions of topoisomerase II that are important for drug action and identified sites near the active site tyrosine that contribute to drug sensitivity. Interestingly, we also identified amino acids near the C-terminal dimerization domain that also control DNA cleavage. Mutations in the C-terminal dimerization domain exhibit several unique characteristics. Importantly, we identified two mutants in the dimerization domain of yeast Top2 that could not be viably expressed in yeast mutants defective in double strand break repair. Expression of these mutants in repair proficient strains led to elevated rates of homologous recombination, suggesting that these mutant proteins are able to generate DNA damage even in the absence of topoisomerase II targeting agents. We purified the mutant proteins and demonstrated that they possess elevated levels of drug independent DNA cleavage, compared to wild type proteins. Elevated cleavage was only seen in the presence of ATP, indicating that the mutant proteins are likely defective in DNA religation at a specific step in the catalytic cycle, and that the C-terminal dimerization and DNA religation occurs by a coordinated process. Finally, we have also shown that homologous mutations in human topoisomerase II alpha generate effects similar to those described for the yeast protein. Taken together, these results suggest that it may be possible to identify potent allosteric inhibitors of topoisomerase II directed against the C-terminal catalytic domain of the protein. These hypothetical inhibitors may have unique therapeutic potential, especially because they represent an approach for isoform specific topoisomerase poisons. Citation Format: Anna Rogojina, Karin C. Nitiss, John L. Nitiss. New approaches to changing an enzyme into a cytotoxic agent: A novel way to stimulate DNA cleavage by topoisomerase II. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4480. doi:10.1158/1538-7445.AM2013-4480

Topoisomerase IIα promotes activation of RNA polymerase I transcription by facilitating pre-initiation complex formation

Type II DNA topoisomerases catalyse DNA double-strand cleavage, passage and re-ligation to effect topological changes. There is considerable interest in elucidating topoisomerase II roles, particularly as these proteins are targets for anti-cancer drugs. Here we uncover a role for topoisomerase IIα in RNA polymerase I-directed ribosomal RNA gene transcription, which drives cell growth and proliferation and is upregulated in cancer cells. Our data suggest that topoisomerase IIα is a component of the initiation-competent RNA polymerase Iβ complex and interacts directly with RNA polymerase I-associated transcription factor RRN3, which targets the polymerase to promoter-bound SL1 in pre-initiation complex formation. In cells, activation of rDNA transcription is reduced by inhibition or depletion of topoisomerase II, and this is accompanied by reduced transient double-strand DNA cleavage in the rDNA-promoter region and reduced pre-initiation complex formation. We propose that topoisomerase IIα functions in RNA polymerase I transcription to produce topological changes at the rDNA promoter that facilitate efficient de novo pre-initiation complex formation.

Generation of assays and antibodies to facilitate the study of human 5′-tyrosyl DNA phosphodiesterase

Topoisomerases regulate DNA topology by the transient cleavage and religation of DNA during transcription and replication. Topoisomerase II (Topo II) poisons such as etoposide can induce abortive DNA strand breaks in which Topo II remains covalently bound to a 5′ DNA strand terminus via a phosphotyrosyl linker. Tyrosyl DNA phosphodiesterase 2 (Tdp2) is a recently discovered human 5′-tyrosyl DNA phosphodiesterase that repairs this topoisomerase-mediated DNA damage, thereby playing a central role in maintaining normal DNA topology in cells. Cellular depletion of Tdp2 has been shown to result in increased susceptibility and sensitivity to Topo II-induced DNA double-strand breaks, thereby revealing Tdp2 as a potentially attractive anticancer target. No drug-like inhibitors of Tdp2 have been identified to date, and assays suitable for high-throughput screening (HTS) have not been widely reported. Here we have identified a new and effective chromogenic substrate for Tdp2 and developed a homogeneous and robust HTS assay. A second novel Tdp2 assay was also developed to cross-validate hit matter identified from an HTS. In addition, a new and specific Tdp2 antibody is described. Together, these new tools will aid in the identification of novel Tdp2 inhibitors and the investigation of the role of Tdp2 in cancer.

Chemical Mutagenesis of Vaccinia DNA Topoisomerase Lysine 167 Provides Insights to the Catalysis of DNA Transesterification

Vaccinia DNA topoisomerase IB (TopIB) relaxes supercoils by forming and resealing a covalent DNA-(3'-phosphotyrosyl(274))-enzyme intermediate. Conserved active site side chains promote the attack of Tyr274 on the scissile phosphodiester via transition state stabilization and general acid catalysis. Two essential side chains, Lys167 and Arg130, act in concert to protonate and expel the 5'-O leaving group. Here we gained new insights to catalysis through chemical mutagenesis of Lys167. Changing Lys167 to cysteine crippled the DNA cleavage and religation transesterification steps (k(cl) = 4.3 × 10(-4) s(-1); k(rel) = 9 × 10(-4) s(-1)). The transesterification activities of the K167C enzyme were revived by in vitro alkylation with 2-bromoethylamine (k(cl) = 0.031 s(-1); k(rel) ≥ 0.4 s(-1)) and 3-bromopropylamine (k(cl) = 0.013 s(-1); k(rel) = 0.22 s(-1)), which convert the cysteines to γ-thialysine and γ-thiahomolysine, respectively. These chemically installed lysine analogues were more effective than a genetically programmed arginine 167 substitution characterized previously. The modest differences in the transesterification rates of the 2-bromoethylamine- and 3-bromopropylamine-treated enzymes highlight that TopIB is tolerant of a longer homolysine side chain for assembly of the active site and formation of the transition state.