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Kornienko TE, Chepanova AA, Zakharenko AL, Filimonov AS, Luzina OA, Dyrkheeva NS, Nikolin VP, Popova NA, Salakhutdinov NF, Lavrik OI. Enhancement of the Antitumor and Antimetastatic Effect of Topotecan and Normalization of Blood Counts in Mice with Lewis Carcinoma by Tdp1 Inhibitors-New Usnic Acid Derivatives. Int J Mol Sci 2024; 25:1210. [PMID: 38279210 PMCID: PMC10816808 DOI: 10.3390/ijms25021210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is an important DNA repair enzyme and one of the causes of tumor resistance to topoisomerase 1 inhibitors such as topotecan. Inhibitors of this Tdp1 in combination with topotecan may improve the effectiveness of therapy. In this work, we synthesized usnic acid derivatives, which are hybrids of its known derivatives: tumor sensitizers to topotecan. New compounds inhibit Tdp1 in the micromolar and submicromolar concentration range; some of them enhance the effect of topotecan on the metabolic activity of cells of various lines according to the MTT test. One of the new compounds (compound 7) not only sensitizes Krebs-2 and Lewis carcinomas of mice to the action of topotecan, but also normalizes the state of the peripheral blood of mice, which is disturbed in the presence of a tumor. Thus, the synthesized substances may be the prototype of a new class of additional therapy for cancer.
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Affiliation(s)
- Tatyana E. Kornienko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (T.E.K.); (A.A.C.); (N.S.D.); (O.I.L.)
| | - Arina A. Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (T.E.K.); (A.A.C.); (N.S.D.); (O.I.L.)
| | - Alexandra L. Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (T.E.K.); (A.A.C.); (N.S.D.); (O.I.L.)
| | - Aleksandr S. Filimonov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (A.S.F.); (O.A.L.); (N.F.S.)
| | - Olga A. Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (A.S.F.); (O.A.L.); (N.F.S.)
| | - Nadezhda S. Dyrkheeva
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (T.E.K.); (A.A.C.); (N.S.D.); (O.I.L.)
| | - Valeriy P. Nikolin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (V.P.N.); (N.A.P.)
| | - Nelly A. Popova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (V.P.N.); (N.A.P.)
| | - Nariman F. Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (A.S.F.); (O.A.L.); (N.F.S.)
| | - Olga I. Lavrik
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (T.E.K.); (A.A.C.); (N.S.D.); (O.I.L.)
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2
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Zakharenko AL, Luzina OA, Chepanova AA, Dyrkheeva NS, Salakhutdinov NF, Lavrik OI. Natural Products and Their Derivatives as Inhibitors of the DNA Repair Enzyme Tyrosyl-DNA Phosphodiesterase 1. Int J Mol Sci 2023; 24:5781. [PMID: 36982848 PMCID: PMC10051138 DOI: 10.3390/ijms24065781] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/22/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is an important repair enzyme that removes various covalent adducts from the 3' end of DNA. Particularly, covalent complexes of topoisomerase 1 (TOP1) with DNA stabilized by DNA damage or by various chemical agents are an examples of such adducts. Anticancer drugs such as the TOP1 poisons topotecan and irinotecan are responsible for the stabilization of these complexes. TDP1 neutralizes the effect of these anticancer drugs, eliminating the DNA adducts. Therefore, the inhibition of TDP1 can sensitize tumor cells to the action of TOP1 poisons. This review contains information about methods for determining the TDP1 activity, as well as describing the inhibitors of these enzyme derivatives of natural biologically active substances, such as aminoglycosides, nucleosides, polyphenolic compounds, and terpenoids. Data on the efficiency of combined inhibition of TOP1 and TDP1 in vitro and in vivo are presented.
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Affiliation(s)
- Alexandra L. Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Olga A. Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Arina A. Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Nadezhda S. Dyrkheeva
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Nariman F. Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Olga I. Lavrik
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia
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3
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Dyrkheeva NS, Malakhova AA, Zakharenko AL, Okorokova LS, Shtokalo DN, Pavlova SV, Medvedev SP, Zakian SM, Nushtaeva AA, Tupikin AE, Kabilov MR, Khodyreva SN, Luzina OA, Salakhutdinov NF, Lavrik OI. Transcriptomic Analysis of CRISPR/Cas9-Mediated PARP1-Knockout Cells under the Influence of Topotecan and TDP1 Inhibitor. Int J Mol Sci 2023; 24:ijms24065148. [PMID: 36982223 PMCID: PMC10049738 DOI: 10.3390/ijms24065148] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Topoisomerase 1 (TOP1) is an enzyme that regulates DNA topology and is essential for replication, recombination, and other processes. The normal TOP1 catalytic cycle involves the formation of a short-lived covalent complex with the 3' end of DNA (TOP1 cleavage complex, TOP1cc), which can be stabilized, resulting in cell death. This fact substantiates the effectiveness of anticancer drugs-TOP1 poisons, such as topotecan, that block the relegation of DNA and fix TOP1cc. Tyrosyl-DNA phosphodiesterase 1 (TDP1) is able to eliminate TOP1cc. Thus, TDP1 interferes with the action of topotecan. Poly(ADP-ribose) polymerase 1 (PARP1) is a key regulator of many processes in the cell, such as maintaining the integrity of the genome, regulation of the cell cycle, cell death, and others. PARP1 also controls the repair of TOP1cc. We performed a transcriptomic analysis of wild type and PARP1 knockout HEK293A cells treated with topotecan and TDP1 inhibitor OL9-119 alone and in combination. The largest number of differentially expressed genes (DEGs, about 4000 both up- and down-regulated genes) was found in knockout cells. Topotecan and OL9-119 treatment elicited significantly fewer DEGs in WT cells and negligible DEGs in PARP1-KO cells. A significant part of the changes caused by PARP1-KO affected the synthesis and processing of proteins. Differences under the action of treatment with TOP1 or TDP1 inhibitors alone were found in the signaling pathways for the development of cancer, DNA repair, and the proteasome. The drug combination resulted in DEGs in the ribosome, proteasome, spliceosome, and oxidative phosphorylation pathways.
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Affiliation(s)
- Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Anastasia A Malakhova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Aleksandra L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | | | - Dmitriy N Shtokalo
- AcademGene LLC, 6 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- A.P. Ershov Institute of Informatics Systems SB RAS, 6 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Sophia V Pavlova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Sergey P Medvedev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Suren M Zakian
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Federal Research Centre Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Anna A Nushtaeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Svetlana N Khodyreva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Olga A Luzina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Nariman F Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 Lavrentyeva Ave., 630090 Novosibirsk, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., 630090 Novosibirsk, Russia
- Department of Molecular Biology and Biotechnology, Novosibirsk State University, 630090 Novosibirsk, Russia
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TDP1-independent pathways in the process and repair of TOP1-induced DNA damage. Nat Commun 2022; 13:4240. [PMID: 35869071 PMCID: PMC9307636 DOI: 10.1038/s41467-022-31801-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 06/29/2022] [Indexed: 11/15/2022] Open
Abstract
Anticancer drugs, such as camptothecin (CPT), trap topoisomerase I (TOP1) on DNA and form TOP1 cleavage complexes (TOP1cc). Alternative repair pathways have been suggested in the repair of TOP1cc. However, how these pathways work with TDP1, a key repair enzyme that specifically hydrolyze the covalent bond between TOP1 catalytic tyrosine and the 3’-end of DNA and contribute to the repair of TOP1cc is poorly understood. Here, using unbiased whole-genome CRISPR screens and generation of co-deficient cells with TDP1 and other genes, we demonstrate that MUS81 is an important factor that mediates the generation of excess double-strand breaks (DSBs) in TDP1 KO cells. APEX1/2 are synthetic lethal with TDP1. However, deficiency of APEX1/2 does not reduce DSB formation in TDP1 KO cells. Together, our data suggest that TOP1cc can be either resolved directly by TDP1 or be converted into DSBs and repaired further by the Homologous Recombination (HR) pathway. Here the authors find that MUS81 mediates excess DNA double strand break (DSB) generation in TDP1 KO cells after camptothecin treatment. They show that TOP1 cleavage complexes can be either resolved directly by TDP1 or be converted into DSBs and repaired further by the Homologous Recombination pathway.
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Yang H, Wang FT, Wu M, Wang W, Agama K, Pommier Y, An LK. Synthesis of 11-aminoalkoxy substituted benzophenanthridine derivatives as tyrosyl-DNA phosphodiesterase 1 inhibitors and their anticancer activity. Bioorg Chem 2022; 123:105789. [PMID: 35429714 PMCID: PMC10557912 DOI: 10.1016/j.bioorg.2022.105789] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/02/2022] [Accepted: 03/31/2022] [Indexed: 11/19/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is an enzyme that repairs DNA lesions caused by the trapping of DNA topoisomerase IB (TOP1)-DNA break-associated crosslinks. TDP1 inhibitors have synergistic effect with TOP1 inhibitors in cancer cells and can overcome cancer cell resistance to TOP1 inhibitors. Here, we report the synthesis of 11-aminoalkoxy substituted benzophenanthridine derivatives as selective TDP1 inhibitors and show that six compounds 14, 16, 18, 20, 25 and 27 exhibit high TDP1 inhibition potency. The most potent TDP1 inhibitor 14 (IC50 = 1.7 ± 0.24 μM) induces cellular TDP1cc formation and shows synergistic effect with topotecan in four human cancer cell lines MCF-7, A549, H460 and HepG2.
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Affiliation(s)
- Hao Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Fang-Ting Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Min Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Wenjie Wang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Keli Agama
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou 510006, China.
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Jha JS, Yin J, Haldar T, Wang Y, Gates KS. Reconsidering the Chemical Nature of Strand Breaks Derived from Abasic Sites in Cellular DNA: Evidence for 3'-Glutathionylation. J Am Chem Soc 2022; 144:10471-10482. [PMID: 35612610 DOI: 10.1021/jacs.2c02703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The hydrolytic loss of coding bases from cellular DNA is a common and unavoidable reaction. The resulting abasic sites can undergo β-elimination of the 3'-phosphoryl group to generate a strand break with an electrophilic α,β-unsaturated aldehyde residue on the 3'-terminus. The work reported here provides evidence that the thiol residue of the cellular tripeptide glutathione rapidly adds to the alkenal group on the 3'-terminus of an AP-derived strand break. The resulting glutathionylated adduct is the only major cleavage product observed when β-elimination occurs at an AP site in the presence of glutathione. Formation of the glutathionylated cleavage product is reversible, but in the presence of physiological concentrations of glutathione, the adduct persists for days. Biochemical experiments provided evidence that the 3'-phosphodiesterase activity of the enzyme apurinic/apyrimidinic endonuclease (APE1) can remove the glutathionylated sugar remnant from an AP-derived strand break to generate the 3'OH residue required for repair via base excision or single-strand break repair pathways. The results suggest that a previously unrecognized 3'glutathionylated sugar remnant─and not the canonical α,β-unsaturated aldehyde end group─may be the true strand cleavage product arising from β-elimination at an abasic site in cellular DNA. This work introduces the 3'glutathionylated cleavage product as the major blocking group that must be trimmed to enable repair of abasic site-derived strand breaks by the base excision repair or single-strand break repair pathways.
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TDP1 and TOP1 as targets in anticancer treatment of NSCLC: Activity and protein level in normal and tumor tissue from 150 NSCLC patients correlated to clinical data. Lung Cancer 2021; 164:23-32. [PMID: 34974222 DOI: 10.1016/j.lungcan.2021.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/04/2021] [Accepted: 12/12/2021] [Indexed: 02/08/2023]
Abstract
OBJECTIVES Topoisomerase 1 (TOP1) is a drug target used in anticancer treatment of various cancer types. The effect of the TOP1 drugs can be counteracted by the enzymatic activity of tyrosyl-DNA phosphodiesterase 1 (TDP1). Thus, to elucidate the relevance of combining TDP1 and TOP1 as drug targets for anticancer treatment in NSCLC, TDP1 and TOP1 was for the first time quantified in a large cohort of paired normal and tumor tissue from NSCLC patients, and data were correlated between the two enzymes and to clinical data. MATERIALS AND METHODS TDP1 and TOP1 activity and protein concentration were measured in paired normal and tumor tissue from 150 NSCLC patients using TDP1 and TOP1 specific biosensors and ELISA. TDP1 and TOP1 activity and protein concentration were correlated to clinical data. RESULTS TDP1 and TOP1 activity and protein concentration were significantly upregulated from normal to tumor tissue for the individual patients, but did not correlate to any of the clinical data. TDP1 and TOP1 activity were upregulated in 89.3% and 82.7% of the patients, respectively, and correlated in both normal and tumor tissue. The same tendency was observed for protein concentration with an upregulation of TDP1 and TOP1 in 73.0% and 84.4% of the patients, respectively. The activity and protein concentration correlated in normal and tumor tissue for both TDP1 and TOP1. CONCLUSION The upregulations of TDP1 and TOP1 from normal to tumor tissue combined with the observation that TDP1 and TOP1 did not correlate to any of the clinical data indicate that both proteins are important for development or maintenance of the tumor cells in NSCLC. Correlations between TDP1 and TOP1 indicate a biological dependency and potential co-regulation of the enzymes. These observations is encouraging in relation to using TOP1 and TDP1 as targets in anticancer treatment of NSCLC.
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Kovaleva K, Mamontova E, Yarovaya O, Zakharova O, Zakharenko A, Lavrik O, Salakhutdinov N. Dehydroabietylamine-based thiazolidin-4-ones and 2-thioxoimidazolidin-4-ones as novel tyrosyl-DNA phosphodiesterase 1 inhibitors. Mol Divers 2021; 25:2389-2397. [PMID: 32833106 DOI: 10.1007/s11030-020-10132-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a DNA repair enzyme that plays a key role in repairing damage caused by various antitumor drugs. It is a promising target in medicinal chemistry for the creation of cancer adjuvant therapy. Inhibition of this enzyme together with the use of anticancer chemotherapy enhances the effect of the latter. The natural mutant of TDP1, TDP1(H493R), causes severe neurodegenerative disease spinocerebellar ataxia syndrome with axonal neuropathy (SCAN1). Inhibition of TDP1(H493R) appears to be useful in containment the progression of the disease. A library of compounds was synthesized starting from dehydroabietylamine including heterocyclic pharmacophore groups in the core. To obtain the desired products, the starting dehydroabietylamine was introduced sequentially in reaction with isothiocyanate and ethyl bromoacetate. Different classes of heterocyclic derivatives-2-iminothiazolidin-4-ons and 2-thioxoimidazolidin-4-ones-were obtained depending on the addition order of reagents. 2-Iminothiazolidin-4-thiones were obtained from 2-iminothiazolidin-4-ones under the action of the Lawesson's reagent. Effective TDP1 inhibitors were found among the obtained compounds that work in submicromolar concentrations. The inhibitor of TDP1(H493R) was also detected.
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Affiliation(s)
- Kseniya Kovaleva
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation, 630090.
- Novosibirsk State University, Novosibirsk, Russian Federation, 630090.
| | - Evgeniya Mamontova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation, 630090
| | - Olga Yarovaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation, 630090
- Novosibirsk State University, Novosibirsk, Russian Federation, 630090
| | - Olga Zakharova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation, 630090
| | - Alexandra Zakharenko
- Novosibirsk State University, Novosibirsk, Russian Federation, 630090
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation, 630090
| | - Olga Lavrik
- Novosibirsk State University, Novosibirsk, Russian Federation, 630090
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation, 630090
| | - Nariman Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation, 630090
- Novosibirsk State University, Novosibirsk, Russian Federation, 630090
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9
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Nikolin VP, Popova NA, Kaledin VI, Luzina OA, Zakharenko AL, Salakhutdinov NF, Lavrik OI. The influence of an enamine usnic acid derivative (a tyrosyl-DNA phosphodiesterase 1 inhibitor) on the therapeutic effect of topotecan against transplanted tumors in vivo. Clin Exp Metastasis 2021; 38:431-440. [PMID: 34370156 DOI: 10.1007/s10585-021-10113-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/23/2021] [Indexed: 10/20/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a repair enzyme for 3'-end DNA lesions, predominantly stalled DNA-topoisomerase 1 (Top1) cleavage complexes. Tdp1 is a promising target for anticancer therapy based on DNA damage caused by Top1 poisoning. Earlier, we have reported about usnic acid enamine derivatives that are Tdp1 inhibitors sensitizing tumor cells to the action of Top1 poison (Zakharenko in J Nat Prod 79:2961-2967, 2016). In the present work, we showed a sensitizing effect of an enamine derivative of usnic acid (when administered intragastrically) on Lewis lung carcinoma in mice in combination with topotecan (TPT, Top1 poison used in the clinic). In the presence of the usnic acid derivative, both the volume of the primary tumor and the number of metastases significantly diminished. The absence of acute toxicity of this compound was demonstrated, as was the importance of the method of its administration for the manifestation of the sensitizing properties.
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Affiliation(s)
- V P Nikolin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Akademika Lavrentieva Ave., Novosibirsk, Russian Federation, 630090
| | - N A Popova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Akademika Lavrentieva Ave., Novosibirsk, Russian Federation, 630090
- Novosibirsk State University, 1 Pirogova Str., Novosibirsk, Russian Federation, 630090
| | - V I Kaledin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Akademika Lavrentieva Ave., Novosibirsk, Russian Federation, 630090
| | - O A Luzina
- N. N. Vorozhtsov Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9 Akademika Lavrentieva Ave., Novosibirsk, Russian Federation, 630090
| | - A L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akademika Lavrentieva Ave., Novosibirsk, Russian Federation, 630090
| | - N F Salakhutdinov
- N. N. Vorozhtsov Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9 Akademika Lavrentieva Ave., Novosibirsk, Russian Federation, 630090
- Novosibirsk State University, 1 Pirogova Str., Novosibirsk, Russian Federation, 630090
| | - O I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akademika Lavrentieva Ave., Novosibirsk, Russian Federation, 630090.
- Novosibirsk State University, 1 Pirogova Str., Novosibirsk, Russian Federation, 630090.
- Altai State University, 61 Lenina Ave., Barnaul, Russian Federation, 656049.
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10
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A Dual-Sensor-Based Screening System for In Vitro Selection of TDP1 Inhibitors. SENSORS 2021; 21:s21144832. [PMID: 34300575 PMCID: PMC8309759 DOI: 10.3390/s21144832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022]
Abstract
DNA sensors can be used as robust tools for high-throughput drug screening of small molecules with the potential to inhibit specific enzymes. As enzymes work in complex biological pathways, it is important to screen for both desired and undesired inhibitory effects. We here report a screening system utilizing specific sensors for tyrosyl-DNA phosphodiesterase 1 (TDP1) and topoisomerase 1 (TOP1) activity to screen in vitro for drugs inhibiting TDP1 without affecting TOP1. As the main function of TDP1 is repair of TOP1 cleavage-induced DNA damage, inhibition of TOP1 cleavage could thus reduce the biological effect of the TDP1 drugs. We identified three new drug candidates of the 1,5-naphthyridine and 1,2,3,4-tetrahydroquinolinylphosphine sulfide families. All three TDP1 inhibitors had no effect on TOP1 activity and acted synergistically with the TOP1 poison SN-38 to increase the amount of TOP1 cleavage-induced DNA damage. Further, they promoted cell death even with low dose SN-38, thereby establishing two new classes of TDP1 inhibitors with clinical potential. Thus, we here report a dual-sensor screening approach for in vitro selection of TDP1 drugs and three new TDP1 drug candidates that act synergistically with TOP1 poisons.
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11
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Gladkova ED, Chepanova AA, Ilina ES, Zakharenko AL, Reynisson J, Luzina OA, Volcho KP, Lavrik OI, Salakhutdinov NF. Discovery of Novel Sultone Fused Berberine Derivatives as Promising Tdp1 Inhibitors. Molecules 2021; 26:molecules26071945. [PMID: 33808389 PMCID: PMC8037669 DOI: 10.3390/molecules26071945] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/18/2022] Open
Abstract
A new type of berberine derivatives was obtained by the reaction of berberrubine with aliphatic sulfonyl chlorides. The new polycyclic compounds have a sultone ring condensed to C and D rings of a protoberberine core. The reaction conditions were developed to facilitate the formation of sultones with high yields without by-product formation. Thus, it was shown that the order of addition of reagents affects the composition of the reaction products: when sulfochlorides are added to berberrubine, their corresponding 9-O-sulfonates are predominantly formed; when berberrubine is added to pre-generated sulfenes, sultones are the only products. The reaction was shown to proceed stereo-selectively and the cycle configuration was confirmed by 2D NMR spectroscopy. The inhibitory activity of the synthesized sultones and their 12-brominated analogs against the DNA-repair enzyme tyrosyl-DNA phosphodiesterase 1 (Tdp1), an important target for a potential antitumor therapy, was studied. All derivatives were active in the micromolar and submicromolar range, in contrast to the acyclic analogs and 9-O-sulfonates, which were inactive. The significance of the sultone cycle and bromine substituent in binding with the enzyme was confirmed using molecular modeling. The active inhibitors are mostly non-toxic to the HeLa cancer cell line, and several ligands show synergy with topotecan, a topoisomerase 1 poison in clinical use. Thus, novel berberine derivatives can be considered as candidates for adjuvant therapy against cancer.
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Affiliation(s)
- Elizaveta D. Gladkova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (E.D.G.); (K.P.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
| | - Arina A. Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (E.S.I.); (A.L.Z.); (O.I.L.)
| | - Ekaterina S. Ilina
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (E.S.I.); (A.L.Z.); (O.I.L.)
| | - Alexandra L. Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (E.S.I.); (A.L.Z.); (O.I.L.)
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Staffordshire ST5 5BG, UK;
| | - Olga A. Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (E.D.G.); (K.P.V.)
- Correspondence: (O.A.L.); (N.F.S.)
| | - Konstantin P. Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (E.D.G.); (K.P.V.)
| | - Olga I. Lavrik
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (E.S.I.); (A.L.Z.); (O.I.L.)
| | - Nariman F. Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (E.D.G.); (K.P.V.)
- Correspondence: (O.A.L.); (N.F.S.)
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12
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Zaksauskaite R, Thomas RC, van Eeden F, El-Khamisy SF. Tdp1 protects from topoisomerase 1-mediated chromosomal breaks in adult zebrafish but is dispensable during larval development. SCIENCE ADVANCES 2021; 7:eabc4165. [PMID: 33514542 PMCID: PMC7846158 DOI: 10.1126/sciadv.abc4165] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
Deficiency in the DNA end-processing enzyme, tyrosyl-DNA phosphodiesterase 1 (TDP1), causes progressive neurodegeneration in humans. Here, we generated a tdp1 knockout zebrafish and confirmed the lack of TDP1 activity. In adulthood, homozygotes exhibit hypersensitivity to topoisomerase 1 (Top1) poisons and a very mild locomotion defect. Unexpectedly, embryonic tdp1 -/- zebrafish were not hypersensitive to Top1 poisons and did not exhibit increased Top1-DNA breaks. This is in contrast to the hypersensitivity of Tdp1-deficient vertebrate models reported to date. Tdp1 is dispensable in the zebrafish embryo with transcript levels down-regulated in response to Top1-DNA damage. In contrast, apex2 and ercc4 (xpf) transcripts were up-regulated. These findings identify the tdp1-/- zebrafish embryo as the first vertebrate model that does not require Tdp1 to protect from Top1-DNA damage and identify apex2 and ercc4 (xpf) as putative players fulfilling this role. It highlights the requirement of distinct DNA repair factors across the life span of vertebrates.
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Affiliation(s)
- Ringaile Zaksauskaite
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Ruth C Thomas
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
- Bateson Centre, Department of Biomedical Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Freek van Eeden
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
- Bateson Centre, Department of Biomedical Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Sherif F El-Khamisy
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
- The Institute of Cancer Therapeutics, University of Bradford, Bradford BD7 1DP, UK
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Xiao LG, Zhang Y, Zhang HL, Li D, Gu Q, Tang GH, Yu Q, An LK. Spiroconyone A, a new phytosterol with a spiro [5,6] ring system from Conyza japonica. Org Biomol Chem 2020; 18:5130-5136. [PMID: 32379263 DOI: 10.1039/d0ob00666a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Spiroconyone A (1), the first rearranged phytosterol featuring an unusual spiro [5,6] ring system, and nine known compounds (2-10) were isolated from the aerial parts of Conyza japonica. The structure of 1 was elucidated through spectroscopic methods, and its absolute configuration was determined by single-crystal X-ray diffraction analysis. Enzyme-based assay revealed that spiroconyone A showed weak TDP1 inhibition and compounds 7 and 10 showed TDP1 inhibition with IC50 values of 36 μM and 16 μM, respectively. MTT assay indicated that 7 and 10 showed a strong synergistic effect with the clinical TOP1 inhibitor topotecan in MCF-7 cells. Compound 5 displayed the most potent cytotoxicity against MCF-7 cells with a GI50 value of 3.3 μM. Furthermore, a hypothetical biosynthetic pathway for 1 was proposed. This work provides valuable information that the secondary metabolites from Conyza japonica could be developed as anticancer agents.
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Affiliation(s)
- Long-Gao Xiao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Yu Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Hong-Li Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Ding Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Qiong Gu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Gui-Hua Tang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Qian Yu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China. and Clinical Pharmacy (School of Integrative Pharmacy, Institute of Integrative Pharmaceutical Research), Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China. and Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou, 510006, China
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14
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Tsuda M, Kitamasu K, Kumagai C, Sugiyama K, Nakano T, Ide H. Tyrosyl-DNA phosphodiesterase 2 (TDP2) repairs topoisomerase 1 DNA-protein crosslinks and 3'-blocking lesions in the absence of tyrosyl-DNA phosphodiesterase 1 (TDP1). DNA Repair (Amst) 2020; 91-92:102849. [PMID: 32460231 DOI: 10.1016/j.dnarep.2020.102849] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/19/2020] [Accepted: 03/23/2020] [Indexed: 01/29/2023]
Abstract
Topoisomerase I (TOP1) resolves DNA topology during replication and transcription. The enzyme forms an intermediate TOP1 cleavage complex (TOP1cc) through transient TOP1-DNA-protein crosslinks. Camptothecin is a frontline anticancer agent that freezes this reaction intermediate, leading to the generation of irreversible TOP1ccs that act as 3'-blocking lesions. It is widely accepted that TOP1cc is repaired via a two-step pathway involving proteasomal degradation of TOP1cc to the crosslinked peptide, followed by removal of the TOP1cc-derived peptide from DNA by tyrosyl-DNA phosphodiesterase 1 (TDP1). In the present study, we developed an assay system to estimate repair kinetics of TOP1cc separately in the first and second steps, using monoclonal antibodies against the TOP1 protein and the TOP1 catalytic site peptide-DNA complex, respectively. Although TDP1-deficient (TDP1-/-) TK6 cells had normal kinetics of the first step, a delay in the kinetics of the second step was observed relative to that in wild-type cells. Tyrosyl-DNA phosphodiesterase 2 (TDP2) reportedly promotes the repair of TOP1-induced DNA damage in the absence of TDP1. The present assays additionally demonstrated that TDP2 promotes the second, but not the first, step of TOP1cc repair in the absence of TDP1. We also analyzed sensitivities of TK6 cells with deficiencies in TDP1 and/or TDP2 to agents that produce 3' -blocking lesions. These experiments showed that TDP1-/-TDP2-/- cells were more sensitive to the agents Azidothymidine (zidovudine), Cytarabine, Abacavir, Gemcitabine, and Trifluridine than TDP1-/- or TDP2-/- cells. Taken together, our findings confirm the roles of TDP2 in the repair of 3'-blocking lesions.
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Affiliation(s)
- Masataka Tsuda
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
| | - Kaito Kitamasu
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Chiho Kumagai
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Kazuya Sugiyama
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Toshiaki Nakano
- DNA Damage Chemistry Research Group, Institute for Quantum Life Science, National Institutes of Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa-shi, Kyoto 619-0215, Japan
| | - Hiroshi Ide
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
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15
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Mei C, Lei L, Tan LM, Xu XJ, He BM, Luo C, Yin JY, Li X, Zhang W, Zhou HH, Liu ZQ. The role of single strand break repair pathways in cellular responses to camptothecin induced DNA damage. Biomed Pharmacother 2020; 125:109875. [DOI: 10.1016/j.biopha.2020.109875] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/24/2019] [Accepted: 01/06/2020] [Indexed: 12/12/2022] Open
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16
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Brettrager EJ, van Waardenburg RC. Targeting Tyrosyl-DNA phosphodiesterase I to enhance toxicity of phosphodiester linked DNA-adducts. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2019; 2:1153-1163. [PMID: 31875206 PMCID: PMC6929713 DOI: 10.20517/cdr.2019.91] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/19/2019] [Accepted: 11/29/2019] [Indexed: 06/10/2023]
Abstract
Our genomic DNA is under constant assault from endogenous and exogenous sources, which needs to be resolved to maintain cellular homeostasis. The eukaryotic DNA repair enzyme Tyrosyl-DNA phosphodiesterase I (Tdp1) catalyzes the hydrolysis of phosphodiester bonds that covalently link adducts to DNA-ends. Tdp1 utilizes two catalytic histidines to resolve a growing list of DNA-adducts. These DNA-adducts can be divided into two groups: small adducts, including oxidized nucleotides, RNA, and non-canonical nucleoside analogs, and large adducts, such as (drug-stabilized) topoisomerase- DNA covalent complexes or failed Schiff base reactions as occur between PARP1 and DNA. Many Tdp1 substrates are generated by chemotherapeutics linking Tdp1 to cancer drug resistance, making a compelling argument to develop small molecules that target Tdp1 as potential novel therapeutic agents. Tdp1's unique catalytic cycle, which is centered on the formation of Tdp1-DNA covalent reaction intermediate, allows for two principally different targeting strategies: (1) catalytic inhibition of Tdp1 catalysis to prevent Tdp1-mediated repair of DNA-adducts that enhances the effectivity of chemotherapeutics; and (2) poisoning of Tdp1 by stabilization of the Tdp1- DNA covalent reaction intermediate, which would increase the half-life of a potentially toxic DNA-adduct by preventing its resolution, analogous to topoisomerase targeted poisons such as topotecan or etoposide. The catalytic Tdp1 mutant that forms the molecular basis of the autosomal recessive neurodegenerative disease spinocerebellar ataxia with axonal neuropathy best illustrates this concept; however, no small molecules have been reported for this strategy. Herein, we concisely discuss the development of Tdp1 catalytic inhibitors and their results.
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Affiliation(s)
- Evan J. Brettrager
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294-0019, USA
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17
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Mamontova EM, Zakharenko AL, Zakharova OD, Dyrkheeva NS, Volcho KP, Reynisson J, Arabshahi HJ, Salakhutdinov NF, Lavrik OI. Identification of novel inhibitors for the tyrosyl-DNA-phosphodiesterase 1 (Tdp1) mutant SCAN1 using virtual screening. Bioorg Med Chem 2019; 28:115234. [PMID: 31831297 DOI: 10.1016/j.bmc.2019.115234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 10/25/2022]
Abstract
Spinocerebellar ataxia syndrome with axonal neuropathy (SCAN1) is a debilitating neurological disease that is caused by the mutation the Tyrosyl-DNA phosphodiesterase 1 (TDP1) DNA repair enzyme. The crucial His493 in TDP1's binding site is replaced with an arginine amino acid residue rendering the enzyme dysfunctional. A virtual screen was performed against the homology model of SCAN1 and seventeen compounds were identified and tested in a novel SCAN1 specific biochemical assay. Six compounds showed activity with IC50 values between 3.5 and 25.1 µM. The most active ligand 5 (3.5 µM) is a dicoumarin followed by a close structural analogue 6 at 6.0 µM. A less potent series of β-carbolines (14 and 15) was found with potency in the mid-teens. According to molecular modelling an excellent fit for the active ligands into the binding pocket is predicted. To the best of our knowledge, data on inhibitors of the mutant form of TDP1 has not been reported previously. The virtual hits were also tested for wild type TDP1 activity and all six SCAN1 inhibitors are potent for the former, e.g., ligand 5 has a measured IC50 at 99 nM. In the last decade, TDP1 is considered as a promising target for adjuvant therapy against cancer in combination with Topoisomerase 1 poisons. The active ligands are mostly non-toxic to cancer cell lines A-549, T98G and MCF-7 as well as the immortalized WI-38 human fetal lung cells. Furthermore, ligands 5 and 7, show promising synergy in conjunction with topotecan, a clinically used topoisomerase 1 anticancer drug. The active ligands 5, 7, 14 and 15 have a good balance of the physicochemical properties required for oral bioavailability making the excellent candidates for further development.
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Affiliation(s)
- E M Mamontova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk 630090, Russian Federation; Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russian Federation
| | - A L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk 630090, Russian Federation
| | - O D Zakharova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk 630090, Russian Federation
| | - N S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk 630090, Russian Federation
| | - K P Volcho
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russian Federation; N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9, Lavrentiev Ave., Novosibirsk 630090, Russian Federation
| | - J Reynisson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand; School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Staffordshire ST5 5BG, United Kingdom
| | - H J Arabshahi
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - N F Salakhutdinov
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russian Federation; N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9, Lavrentiev Ave., Novosibirsk 630090, Russian Federation
| | - O I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk 630090, Russian Federation.
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UCHL3 Regulates Topoisomerase-Induced Chromosomal Break Repair by Controlling TDP1 Proteostasis. Cell Rep 2019; 23:3352-3365. [PMID: 29898404 PMCID: PMC6019701 DOI: 10.1016/j.celrep.2018.05.033] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 04/17/2018] [Accepted: 05/11/2018] [Indexed: 11/21/2022] Open
Abstract
Genomic damage can feature DNA-protein crosslinks whereby their acute accumulation is utilized to treat cancer and progressive accumulation causes neurodegeneration. This is typified by tyrosyl DNA phosphodiesterase 1 (TDP1), which repairs topoisomerase-mediated chromosomal breaks. Although TDP1 levels vary in multiple clinical settings, the mechanism underpinning this variation is unknown. We reveal that TDP1 is controlled by ubiquitylation and identify UCHL3 as the deubiquitylase that controls TDP1 proteostasis. Depletion of UCHL3 increases TDP1 ubiquitylation and turnover rate and sensitizes cells to TOP1 poisons. Overexpression of UCHL3, but not a catalytically inactive mutant, suppresses TDP1 ubiquitylation and turnover rate. TDP1 overexpression in the topoisomerase therapy-resistant rhabdomyosarcoma is driven by UCHL3 overexpression. In contrast, UCHL3 is downregulated in spinocerebellar ataxia with axonal neuropathy (SCAN1), causing elevated levels of TDP1 ubiquitylation and faster turnover rate. These data establish UCHL3 as a regulator of TDP1 proteostasis and, consequently, a fine-tuner of protein-linked DNA break repair. TDP1 proteostasis is controlled by a UCHL3-dependent ubiquitylation mechanism UCHL3 depletion sensitizes mammalian cells to TOP1 inhibitors Increased TDP1 protein in rhabdomyosarcoma is driven by UCHL3 upregulation Decreased TDP1 protein in spinocerebellar ataxia is driven by UCHL3 downregulation
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Kovaleva K, Oleshko O, Mamontova E, Yarovaya O, Zakharova O, Zakharenko A, Kononova A, Dyrkheeva N, Cheresiz S, Pokrovsky A, Lavrik O, Salakhutdinov N. Dehydroabietylamine Ureas and Thioureas as Tyrosyl-DNA Phosphodiesterase 1 Inhibitors That Enhance the Antitumor Effect of Temozolomide on Glioblastoma Cells. JOURNAL OF NATURAL PRODUCTS 2019; 82:2443-2450. [PMID: 31430155 DOI: 10.1021/acs.jnatprod.8b01095] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A new class of tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors was found among resin acid derivatives. Several novel ureas and thioureas derived from dehydroabietylamine were synthesized and tested for TDP1 inhibition. The synthesized compounds showed IC50 values in the range of 0.1 to 3.7 μM and demonstrated low cytotoxicity against the human tumor cell lines U-937, U-87MG, MDA-MB, SK-Mel8, A-549, MCF7, T98G, and SNB19. Several compounds showed enhancement of the cytotoxic activity of the alkylating agent temozolomide, which is used as a first line therapy against glioblastoma (GBM), in the GBM cell lines U-87MG and SNB19.
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Affiliation(s)
- Kseniya Kovaleva
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
| | - Olga Oleshko
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
| | - Evgeniya Mamontova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
| | - Olga Yarovaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
| | - Olga Zakharova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
| | - Alexandra Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
| | - Alena Kononova
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
| | - Nadezhda Dyrkheeva
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
| | - Sergey Cheresiz
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
- State Scientific Research Institute of Physiology and Basic Medicine , P.O. Box 237, Novosibirsk , 630117 , Russian Federation
| | - Andrey Pokrovsky
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
| | - Olga Lavrik
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
| | - Nariman Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
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Wang W, Rodriguez-Silva M, Acanda de la Rocha AM, Wolf AL, Lai Y, Liu Y, Reinhold WC, Pommier Y, Chambers JW, Tse-Dinh YC. Tyrosyl-DNA Phosphodiesterase 1 and Topoisomerase I Activities as Predictive Indicators for Glioblastoma Susceptibility to Genotoxic Agents. Cancers (Basel) 2019; 11:cancers11101416. [PMID: 31547492 PMCID: PMC6827102 DOI: 10.3390/cancers11101416] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/06/2019] [Accepted: 09/19/2019] [Indexed: 02/06/2023] Open
Abstract
Glioblastoma (GBM) patients have an estimated survival of ~15 months with treatment, and the standard of care only modestly enhances patient survival. Identifying biomarkers representing vulnerabilities may allow for the selection of efficacious chemotherapy options to address personalized variations in GBM tumors. Irinotecan targets topoisomerase I (TOP1) by forming a ternary DNA-TOP1 cleavage complex (TOP1cc), inducing apoptosis. Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a crucial repair enzyme that may reduce the effectiveness of irinotecan. We treated GBM cell lines with increasing concentrations of irinotecan and compared the IC50 values. We found that the TDP1/TOP1 activity ratio had the strongest correlation (Pearson correlation coefficient R = 0.972, based on the average from three sets of experiments) with IC50 values following irinotecan treatment. Increasing the TDP1/TOP1 activity ratio by the ectopic expression of wild-type TDP1 increased in irinotecan IC50, while the expression of the TDP1 catalytic-null mutant did not alter the susceptibility to irinotecan. The TDP1/TOP1 activity ratio may be a new predictive indicator for GBM vulnerability to irinotecan, allowing for the selection of individual patients for irinotecan treatment based on risk-benefit. Moreover, TDP1 inhibitors may be a novel combination treatment with irinotecan to improve GBM patient responsiveness to genotoxic chemotherapies.
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Affiliation(s)
- Wenjie Wang
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Monica Rodriguez-Silva
- Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA.
| | | | - Aizik L Wolf
- Department of Neurosurgery, Miami Neuroscience Center at Larkin, South Miami, FL 33143, USA.
| | - Yanhao Lai
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Yuan Liu
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - William C Reinhold
- Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA.
| | - Yves Pommier
- Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA.
| | - Jeremy W Chambers
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
- Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA.
| | - Yuk-Ching Tse-Dinh
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
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21
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DNA- and DNA-Protein-Crosslink Repair in Plants. Int J Mol Sci 2019; 20:ijms20174304. [PMID: 31484324 PMCID: PMC6747210 DOI: 10.3390/ijms20174304] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/30/2019] [Accepted: 09/01/2019] [Indexed: 12/12/2022] Open
Abstract
DNA-crosslinks are one of the most severe types of DNA lesions. Crosslinks (CLs) can be subdivided into DNA-intrastrand CLs, DNA-interstrand CLs (ICLs) and DNA-protein crosslinks (DPCs), and arise by various exogenous and endogenous sources. If left unrepaired before the cell enters S-phase, ICLs and DPCs pose a major threat to genomic integrity by blocking replication. In order to prevent the collapse of replication forks and impairment of cell division, complex repair pathways have emerged. In mammals, ICLs are repaired by the so-called Fanconi anemia (FA) pathway, which includes 22 different FANC genes, while in plants only a few of these genes are conserved. In this context, two pathways of ICL repair have been defined, each requiring the interaction of a helicase (FANCJB/RTEL1) and a nuclease (FAN1/MUS81). Moreover, homologous recombination (HR) as well as postreplicative repair factors are also involved. Although DPCs possess a comparable toxic potential to cells, it has only recently been shown that at least three parallel pathways for DPC repair exist in plants, defined by the protease WSS1A, the endonuclease MUS81 and tyrosyl-DNA phosphodiesterase 1 (TDP1). The importance of crosslink repair processes are highlighted by the fact that deficiencies in the respective pathways are associated with diverse hereditary disorders.
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22
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Kawale AS, Povirk LF. Tyrosyl-DNA phosphodiesterases: rescuing the genome from the risks of relaxation. Nucleic Acids Res 2019; 46:520-537. [PMID: 29216365 PMCID: PMC5778467 DOI: 10.1093/nar/gkx1219] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 11/29/2017] [Indexed: 12/13/2022] Open
Abstract
Tyrosyl–DNA Phosphodiesterases 1 (TDP1) and 2 (TDP2) are eukaryotic enzymes that clean-up after aberrant topoisomerase activity. While TDP1 hydrolyzes phosphotyrosyl peptides emanating from trapped topoisomerase I (Top I) from the 3′ DNA ends, topoisomerase 2 (Top II)-induced 5′-phosphotyrosyl residues are processed by TDP2. Even though the canonical functions of TDP1 and TDP2 are complementary, they exhibit little structural or sequence similarity. Homozygous mutations in genes encoding these enzymes lead to the development of severe neurodegenerative conditions due to the accumulation of transcription-dependent topoisomerase cleavage complexes underscoring the biological significance of these enzymes in the repair of topoisomerase–DNA lesions in the nervous system. TDP1 can promiscuously process several blocked 3′ ends generated by DNA damaging agents and nucleoside analogs in addition to hydrolyzing 3′-phosphotyrosyl residues. In addition, deficiency of these enzymes causes hypersensitivity to anti-tumor topoisomerase poisons. Thus, TDP1 and TDP2 are promising therapeutic targets and their inhibitors are expected to significantly synergize the effects of current anti-tumor therapies including topoisomerase poisons and other DNA damaging agents. This review covers the structural aspects, biology and regulation of these enzymes, along with ongoing developments in the process of discovering safe and effective TDP inhibitors.
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Affiliation(s)
- Ajinkya S Kawale
- Department of Pharmacology and Toxicology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Lawrence F Povirk
- Department of Pharmacology and Toxicology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
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23
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Enderle J, Dorn A, Beying N, Trapp O, Puchta H. The Protease WSS1A, the Endonuclease MUS81, and the Phosphodiesterase TDP1 Are Involved in Independent Pathways of DNA-protein Crosslink Repair in Plants. THE PLANT CELL 2019; 31:775-790. [PMID: 30760561 PMCID: PMC6501609 DOI: 10.1105/tpc.18.00824] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/08/2019] [Accepted: 02/11/2019] [Indexed: 05/04/2023]
Abstract
DNA-protein crosslinks (DPCs) represent a severe threat to the genome integrity; however, the main mechanisms of DPC repair were only recently elucidated in humans and yeast. Here we define the pathways for DPC repair in plants. Using CRISPR/Cas9, we could show that only one of two homologs of the universal repair proteases SPARTAN/ weak suppressor of smt3 (Wss1), WSS1A, is essential for DPC repair in Arabidopsis (Arabidopsis thaliana). WSS1A defective lines exhibit developmental defects and are hypersensitive to camptothecin (CPT) and cis-platin. Interestingly, the CRISPR/Cas9 mutants of TYROSYL-DNA PHOSPHODIESTERASE 1 (TDP1) are insensitive to CPT, and only the wss1A tdp1 double mutant reveals a higher sensitivity than the wss1A single mutant. This indicates that TDP1 defines a minor backup pathway in the repair of DPCs. Moreover, we found that knock out of the endonuclease METHYL METHANESULFONATE AND UV SENSITIVE PROTEIN 81 (MUS81) results in a strong sensitivity to DPC-inducing agents. The fact that wss1A mus81 and tdp1 mus81 double mutants exhibit growth defects and an increase in dead cells in root meristems after CPT treatment demonstrates that there are three independent pathways for DPC repair in Arabidopsis. These pathways are defined by their different biochemical specificities, as main actors, the DNA endonuclease MUS81 and the protease WSS1A, and the phosphodiesterase TDP1 as backup.
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Affiliation(s)
- Janina Enderle
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe 76131, Germany
| | - Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe 76131, Germany
| | - Natalja Beying
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe 76131, Germany
| | - Oliver Trapp
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe 76131, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe 76131, Germany
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24
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Zhang XR, Wang HW, Tang WL, Zhang Y, Yang H, Hu DX, Ravji A, Marchand C, Kiselev E, Ofori-Atta K, Agama K, Pommier Y, An LK. Discovery, Synthesis, and Evaluation of Oxynitidine Derivatives as Dual Inhibitors of DNA Topoisomerase IB (TOP1) and Tyrosyl-DNA Phosphodiesterase 1 (TDP1), and Potential Antitumor Agents. J Med Chem 2018; 61:9908-9930. [PMID: 30336023 DOI: 10.1021/acs.jmedchem.8b00639] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a recently discovered enzyme repairing DNA lesions resulting from stalled topoisomerase IB (TOP1)-DNA covalent complex. Inhibiting TDP1 in conjunction with TOP1 inhibitors can boost the action of the latter. Herein, we report the discovery of the natural product oxynitidine scaffold as a novel chemotype for the development of TOP1 and TDP1 inhibitors. Three kinds of analogues, benzophenanthridinone, dihydrobenzophenanthridine, and benzophenanthridine derivatives, were synthesized and evaluated for both TOP1 and TDP1 inhibition and cytotoxicity. Analogue 19a showed high TOP1 inhibition (+++) and induced the formation of cellular TOP1cc and DNA damage, resulting in cancer cells apoptosis at nanomolar concentration range. In vivo studies indicated that 19a exhibits antitumor efficiency in HCT116 xenograft model. 41a exhibited additional TDP1 inhibition with IC50 value of 7 μM and synergistic effect with camptothecin in MCF-7 cells. This work will facilitate future efforts for the discovery of natural product-based TOP1 and TDP1 inhibitors.
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Affiliation(s)
- Xiao-Ru Zhang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - Hao-Wen Wang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - Wen-Lin Tang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - Yu Zhang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - Hui Yang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - De-Xuan Hu
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - Azhar Ravji
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Evgeny Kiselev
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Kwabena Ofori-Atta
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Keli Agama
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Lin-Kun An
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
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25
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Zakharenko AL, Luzina OA, Sokolov DN, Kaledin VI, Nikolin VP, Popova NA, Patel J, Zakharova OD, Chepanova AA, Zafar A, Reynisson J, Leung E, Leung IKH, Volcho KP, Salakhutdinov NF, Lavrik OI. Novel tyrosyl-DNA phosphodiesterase 1 inhibitors enhance the therapeutic impact of topoteсan on in vivo tumor models. Eur J Med Chem 2018; 161:581-593. [PMID: 30396105 DOI: 10.1016/j.ejmech.2018.10.055] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/18/2018] [Accepted: 10/22/2018] [Indexed: 02/07/2023]
Abstract
The druggability of the tyrosyl-DNA phosphodiesterase 1 (Tdp1) enzyme was investigated in conjunction with topoisomerase 1 inhibition. A novel class of thiazole, aminothiazole and hydrazonothiazole usnic acid derivatives was synthesized and evaluated as Tdp1 inhibitors and their ability to sensitize tumors to topotecan, a topoisomerase inhibitor in clinical use. Of all the compounds tested, four hydrazinothiazole derivatives, 20c, 20d, 20h and 20i, inhibited the enzyme in the nanomolar range. The activity of the compounds was verified by affinity experiments as well as supported by molecular modelling. The most effective Tdp1 inhibitor, 20d, was ton-toxic and increased the effect of topotecan both in vitro and in vivo in the Lewis lung carcinoma model. Furthermore, 20d showed significant increase in the antitumor and antimetastatic effect of topotecan in mice. The results presented here justify compound 20d to be considered as a drug lead for antitumor therapy.
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Affiliation(s)
- A L Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - O A Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - D N Sokolov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - V I Kaledin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - V P Nikolin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - N A Popova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogova str. 1, Novosibirsk, 630090, Russian Federation
| | - J Patel
- School of Chemical Sciences, The University of Auckland, New Zealand
| | - O D Zakharova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - A A Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - A Zafar
- School of Chemical Sciences, The University of Auckland, New Zealand
| | - J Reynisson
- School of Chemical Sciences, The University of Auckland, New Zealand
| | - E Leung
- Auckland Cancer Society Research Centre and Department of Molecular Medicine and Pathology, The University of Auckland, New Zealand
| | - I K H Leung
- School of Chemical Sciences, The University of Auckland, New Zealand
| | - K P Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogova str. 1, Novosibirsk, 630090, Russian Federation
| | - N F Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogova str. 1, Novosibirsk, 630090, Russian Federation
| | - O I Lavrik
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogova str. 1, Novosibirsk, 630090, Russian Federation.
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26
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Salomatina OV, Popadyuk II, Zakharenko AL, Zakharova OD, Fadeev DS, Komarova NI, Reynisson J, Arabshahi HJ, Chand R, Volcho KP, Salakhutdinov NF, Lavrik OI. Novel Semisynthetic Derivatives of Bile Acids as Effective Tyrosyl-DNA Phosphodiesterase 1 Inhibitors. Molecules 2018; 23:molecules23030679. [PMID: 29562592 PMCID: PMC6017735 DOI: 10.3390/molecules23030679] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 03/14/2018] [Accepted: 03/16/2018] [Indexed: 12/20/2022] Open
Abstract
An Important task in the treatment of oncological and neurodegenerative diseases is the search for new inhibitors of DNA repair system enzymes. Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is one of the DNA repair system enzymes involved in the removal of DNA damages caused by topoisomerase I inhibitors. Thus, reducing the activity of Tdp1 can increase the effectiveness of currently used anticancer drugs. We describe here a new class of semisynthetic small molecule Tdp1 inhibitors based on the bile acid scaffold that were originally identified by virtual screening. The influence of functional groups of bile acids (hydroxy and acetoxy groups in the steroid framework and amide fragment in the side chain) on inhibitory activity was investigated. In vitro studies demonstrate the ability of the semisynthetic derivatives to effectively inhibit Tdp1 with IC50 up to 0.29 µM. Furthermore, an excellent fit is realized for the ligands when docked into the active site of the Tdp1 enzyme.
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Affiliation(s)
- Oksana V Salomatina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, acad. Lavrentjev ave. 9, Novosibirsk 630090, Russia.
| | - Irina I Popadyuk
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, acad. Lavrentjev ave. 9, Novosibirsk 630090, Russia.
| | - Alexandra L Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, SB RAS, acad. Lavrentjev ave. 8, Novosibirsk 630090, Russia.
| | - Olga D Zakharova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, SB RAS, acad. Lavrentjev ave. 8, Novosibirsk 630090, Russia.
| | - Dmitriy S Fadeev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, acad. Lavrentjev ave. 9, Novosibirsk 630090, Russia.
| | - Nina I Komarova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, acad. Lavrentjev ave. 9, Novosibirsk 630090, Russia.
| | - Jóhannes Reynisson
- School of Chemical Sciences, University of Auckland, Auckland 1142, New Zealand.
| | - H John Arabshahi
- School of Chemical Sciences, University of Auckland, Auckland 1142, New Zealand.
| | - Raina Chand
- School of Chemical Sciences, University of Auckland, Auckland 1142, New Zealand.
| | - Konstantin P Volcho
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, acad. Lavrentjev ave. 9, Novosibirsk 630090, Russia.
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia.
| | - Nariman F Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, acad. Lavrentjev ave. 9, Novosibirsk 630090, Russia.
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia.
| | - Olga I Lavrik
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, SB RAS, acad. Lavrentjev ave. 8, Novosibirsk 630090, Russia.
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia.
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27
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Zakharenko AL, Lebedeva NA, Lavrik OI. DNA Repair Enzymes as Promising Targets in Oncotherapy. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162017060140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Reactive oxygen species stress increases accumulation of tyrosyl-DNA phsosphodiesterase 1 within mitochondria. Sci Rep 2018. [PMID: 29523818 PMCID: PMC5844879 DOI: 10.1038/s41598-018-22547-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a nuclear and mitochondrial protein that in nuclei and in vitro repairs blocked 3' DNA termini such as 3' phosphotyrosine conjugates resulting from stalling of topoisomerase I-DNA intermediates. Its mutation also causes spinocerebellar ataxia with axonal neuropathy type 1 (SCAN1). Because Tdp1 colocalizes with mitochondria following oxidative stress, we hypothesized that Tdp1 repairs mitochondrial DNA (mtDNA) and that mtDNA damage mediates entry of Tdp1 into the mitochondria. To test this, we used S. cerevisiae mutants, cultured mouse and human cells, and a Tdp1 knockout mouse. H2O2- and rotenone-induced cellular and intramitochondrial reactive oxygen species (ROS) activated oxidant-responsive kinases P38 and ERK1, and the translocation of Tdp1 from the nucleus to the mitochondria via the TIM/TOM complex. This translocation occurred independently of mtDNA. Within the mitochondria, Tdp1 interacted with Ligase III and reduced mtDNA mutations. Tdp1-deficient tissues had impaired mitochondrial respiration and decreased viability. These observations suggest that Tdp1 maintains mtDNA integrity and support the hypothesis that mitochondrial dysfunction contributes to the pathology of SCAN1.
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29
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Chiang SC, Liversidge K, El-Khamisy SF. Studying TDP1 Function in DNA Repair. Methods Mol Biol 2018; 1703:173-181. [PMID: 29177742 DOI: 10.1007/978-1-4939-7459-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Topoisomerase poisons act by inducing abortive topoisomerase reactions, which generate stable protein-DNA breaks (PDBs) that interfere with transcription elongation and progression of replication forks. In vertebrates, Tyrosyl-DNA phosphodiesterase 1 (TDP1) plays a major role in removal of topoisomerase 1-associated PDBs in the nucleus and mitochondria by hydrolyzing the 3'-phosphotyrosine bond. Depletion of TDP1 sensitizes tumor cells with defective DNA repair capacity to the genotoxic effect of TOP1 poisons, while homozygous mutation of the catalytic residue of TDP1 is associated with cerebellar degeneration and ataxia. We describe here two fluorescence based biochemical assays for measuring TDP1 phosphodiesterase activity in cellular lysates. The Gyrasol assay is sensitive, high-throughput, and useful for screening potential TDP1 inhibitors or cell lines that are likely to develop resistance to TOP1 poisons. The gel-shift assay is low cost and simple to set up, and is also suitable for screening cell lines that are likely to develop resistance to TOP1 poisons, as well as for diagnostic screening for individuals with hereditary ataxias.
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Affiliation(s)
- Shih-Chieh Chiang
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Firth Court, S10 2TN, Sheffield, UK
| | - Kirsty Liversidge
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Firth Court, S10 2TN, Sheffield, UK
| | - Sherif F El-Khamisy
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Firth Court, S10 2TN, Sheffield, UK.
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30
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Horton JK, Stefanick DF, Zhao ML, Janoshazi AK, Gassman NR, Seddon HJ, Wilson SH. XRCC1-mediated repair of strand breaks independent of PNKP binding. DNA Repair (Amst) 2017; 60:52-63. [PMID: 29100039 PMCID: PMC5696015 DOI: 10.1016/j.dnarep.2017.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/03/2017] [Accepted: 10/12/2017] [Indexed: 10/18/2022]
Abstract
Repair of DNA-protein crosslinks and oxidatively damaged DNA base lesions generates intermediates with nicks or gaps with abnormal and blocked 3'-phosphate and 5'-OH ends that prevent the activity of DNA polymerases and ligases. End cleaning in mammalian cells by Tdp1 and PNKP produces the conventional 3'-OH and 5'-phosphate DNA ends suitable for completion of repair. This repair function of PNKP is facilitated by its binding to the scaffold protein XRCC1, and phosphorylation of XRCC1 by CK2 at several consensus sites enables PNKP binding and recruitment to DNA damage. To evaluate this documented repair process, a phosphorylation mutant of XRCC1, designed to eliminate PNKP binding, was stably expressed in Xrcc1-/- mouse fibroblast cells. Analysis of PNKP-GFP accumulation at micro-irradiation induced damage confirmed that the XRCC1 phosphorylation mutant failed to support efficient PNKP recruitment, whereas there was rapid recruitment in cells expressing wild-type XRCC1. Recruitment of additional fluorescently-tagged repair factors PARP-1-YFP, GFF-XRCC1, PNKP-GFP and Tdp1-GFP to micro-irradiation induced damage was assessed in wild-type XRCC1-expressing cells. PARP-1-YFP recruitment was best fit to two exponentials, whereas kinetics for the other proteins were fit to a single exponential. The similar half-times of recruitment suggest that XRCC1 may be recruited with other proteins possibly as a pre-formed complex. Xrcc1-/- cells are hypersensitive to the DNA-protein cross-link inducing agent camptothecin (CPT) and the DNA oxidative agent H2O2 due in part to compromised PNKP-mediated repair. However, cells expressing the PNKP interaction mutant of XRCC1 demonstrated marked reversal of CPT hypersensitivity. This reversal represents XRCC1-dependent repair in the absence of the phosphorylation-dependent PNKP recruitment and suggests either an XRCC1-independent mechanism of PNKP recruitment or a functional back-up pathway for cleaning of blocked DNA ends.
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Affiliation(s)
- Julie K Horton
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Donna F Stefanick
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Ming-Lang Zhao
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Agnes K Janoshazi
- Signal Transduction Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Natalie R Gassman
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Hannah J Seddon
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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31
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Li J, Summerlin M, Nitiss KC, Nitiss JL, Hanakahi LA. TDP1 is required for efficient non-homologous end joining in human cells. DNA Repair (Amst) 2017; 60:40-49. [PMID: 29078113 DOI: 10.1016/j.dnarep.2017.10.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 11/29/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) can remove a wide variety of 3' and 5' terminal DNA adducts. Genetic studies in yeast identified TDP1 as a regulator of non-homologous end joining (NHEJ) fidelity in the repair of double-strand breaks (DSBs) lacking terminal adducts. In this communication, we show that TDP1 plays an important role in joining cohesive DSBs in human cells. To investigate the role of TDP1 in NHEJ in live human cells we used CRISPR/cas9 to produce TDP1-knockout (TDP1-KO) HEK-293 cells. As expected, human TDP1-KO cells were highly sensitive to topoisomerase poisons and ionizing radiation. Using a chromosomally-integrated NHEJ reporter substrate to compare end joining between wild type and TDP1-KO cells, we found that TDP1-KO cells have a 5-fold reduced ability to repair I-SceI-generated DSBs. Extracts prepared from TDP1-KO cells had reduced NHEJ activity in vitro, as compared to extracts from wild type cells. Analysis of end-joining junctions showed that TDP1 deficiency reduced end-joining fidelity, with a significant increase in insertion events, similar to previous observations in yeast. It has been reported that phosphorylation of TDP1 serine 81 (TDP1-S81) by ATM and DNA-PK stabilizes TDP1 and recruits TDP1 to sites of DNA damage. We found that end joining in TDP1-KO cells was partially restored by the non-phosphorylatable mutant TDP1-S81A, but not by the phosphomimetic TDP1-S81E. We previously reported that TDP1 physically interacted with XLF. In this study, we found that XLF binding by TDP1 was reduced 2-fold by the S81A mutation, and 10-fold by the S81E phosphomimetic mutation. Our results demonstrate a novel role for TDP1 in NHEJ in human cells. We hypothesize that TDP1 participation in human NHEJ is mediated by interaction with XLF, and that TDP1-XLF interactions and subsequent NHEJ events are regulated by phosphorylation of TDP1-S81.
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Affiliation(s)
- Jing Li
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 1601 Parkview Ave. Rockford, Chicago, IL, 61107, United States
| | - Matthew Summerlin
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, 1601 Parkview Ave. Rockford, Chicago, IL, 61107, United States
| | - Karin C Nitiss
- Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, 1601 Parkview Ave. Rockford, Chicago, IL, 61107, United States
| | - John L Nitiss
- Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, 1601 Parkview Ave. Rockford, Chicago, IL, 61107, United States
| | - Leslyn A Hanakahi
- Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, 1601 Parkview Ave. Rockford, Chicago, IL, 61107, United States.
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32
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Meisenberg C, Ashour ME, El-Shafie L, Liao C, Hodgson A, Pilborough A, Khurram SA, Downs JA, Ward SE, El-Khamisy SF. Epigenetic changes in histone acetylation underpin resistance to the topoisomerase I inhibitor irinotecan. Nucleic Acids Res 2017; 45:1159-1176. [PMID: 28180300 PMCID: PMC5388393 DOI: 10.1093/nar/gkw1026] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 10/08/2016] [Accepted: 10/18/2016] [Indexed: 02/06/2023] Open
Abstract
The topoisomerase I (TOP1) inhibitor irinotecan triggers cell death by trapping TOP1 on DNA, generating cytotoxic protein-linked DNA breaks (PDBs). Despite its wide application in a variety of solid tumors, the mechanisms of cancer cell resistance to irinotecan remains poorly understood. Here, we generated colorectal cancer (CRC) cell models for irinotecan resistance and report that resistance is neither due to downregulation of the main cellular target of irinotecan TOP1 nor upregulation of the key TOP1 PDB repair factor TDP1. Instead, the faster repair of PDBs underlies resistance, which is associated with perturbed histone H4K16 acetylation. Subsequent treatment of irinotecan-resistant, but not parental, CRC cells with histone deacetylase (HDAC) inhibitors can effectively overcome resistance. Immunohistochemical analyses of CRC tissues further corroborate the importance of histone H4K16 acetylation in CRC. Finally, the resistant clones exhibit cross-resistance with oxaliplatin but not with ionising radiation or 5-fluoruracil, suggesting that the latter two could be employed following loss of irinotecan response. These findings identify perturbed chromatin acetylation in irinotecan resistance and establish HDAC inhibitors as potential therapeutic means to overcome resistance.
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Affiliation(s)
- Cornelia Meisenberg
- Mammalian Genome Stability Group, Krebs and Sheffield Institute for Nucleic Acids, University of Sheffield, Western Bank, Sheffield, UK.,The Wellcome Trust DNA Repair Group, University of Sussex, Brighton, UK
| | - Mohamed E Ashour
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City for Science and Technology, Giza, Egypt.,Mammalian Genome Stability Group, Krebs and Sheffield Institute for Nucleic Acids, University of Sheffield, Western Bank, Sheffield, UK
| | - Lamia El-Shafie
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City for Science and Technology, Giza, Egypt
| | - Chunyan Liao
- Mammalian Genome Stability Group, Krebs and Sheffield Institute for Nucleic Acids, University of Sheffield, Western Bank, Sheffield, UK
| | - Adam Hodgson
- Mammalian Genome Stability Group, Krebs and Sheffield Institute for Nucleic Acids, University of Sheffield, Western Bank, Sheffield, UK
| | - Alice Pilborough
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, University of Sheffield, UK
| | - Syed A Khurram
- Unit of Oral and Maxillofacial Pathology, School of Clinical Dentistry, University of Sheffield, UK
| | - Jessica A Downs
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Simon E Ward
- Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
| | - Sherif F El-Khamisy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City for Science and Technology, Giza, Egypt.,Mammalian Genome Stability Group, Krebs and Sheffield Institute for Nucleic Acids, University of Sheffield, Western Bank, Sheffield, UK.,The Wellcome Trust DNA Repair Group, University of Sussex, Brighton, UK
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33
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Ströbel T, Madlener S, Tuna S, Vose S, Lagerweij T, Wurdinger T, Vierlinger K, Wöhrer A, Price BD, Demple B, Saydam O, Saydam N. Ape1 guides DNA repair pathway choice that is associated with drug tolerance in glioblastoma. Sci Rep 2017; 7:9674. [PMID: 28852018 PMCID: PMC5574897 DOI: 10.1038/s41598-017-10013-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/02/2017] [Indexed: 12/19/2022] Open
Abstract
Ape1 is the major apurinic/apyrimidinic (AP) endonuclease activity in mammalian cells, and a key factor in base-excision repair of DNA. High expression or aberrant subcellular distribution of Ape1 has been detected in many cancer types, correlated with drug response, tumor prognosis, or patient survival. Here we present evidence that Ape1 facilitates BRCA1-mediated homologous recombination repair (HR), while counteracting error-prone non-homologous end joining of DNA double-strand breaks. Furthermore, Ape1, coordinated with checkpoint kinase Chk2, regulates drug response of glioblastoma cells. Suppression of Ape1/Chk2 signaling in glioblastoma cells facilitates alternative means of damage site recruitment of HR proteins as part of a genomic defense system. Through targeting "HR-addicted" temozolomide-resistant glioblastoma cells via a chemical inhibitor of Rad51, we demonstrated that targeting HR is a promising strategy for glioblastoma therapy. Our study uncovers a critical role for Ape1 in DNA repair pathway choice, and provides a mechanistic understanding of DNA repair-supported chemoresistance in glioblastoma cells.
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Affiliation(s)
- Thomas Ströbel
- Institute of Neurology, Medical University of Vienna, A-1090, Vienna, Austria
| | - Sibylle Madlener
- Molecular Neuro-Oncology Research Unit, Department of Pediatrics & Adolescent Medicine, Medical University of Vienna, A-1090, Vienna, Austria
| | - Serkan Tuna
- Molecular Neuro-Oncology Research Unit, Department of Pediatrics & Adolescent Medicine, Medical University of Vienna, A-1090, Vienna, Austria
| | - Sarah Vose
- Vermont Department of Public Health, 108 Cherry St., Burlington, VT, 05402, USA
| | - Tonny Lagerweij
- Neuro-Oncology Research Group, Department of Neurosurgery, VU University Medical Center, Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Thomas Wurdinger
- Neuro-Oncology Research Group, Department of Neurosurgery, VU University Medical Center, Amsterdam, 1081 HV, Amsterdam, The Netherlands.,Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Klemens Vierlinger
- Molecular Diagnostics, AIT - Austrian Institute of Technology, A-1190, Vienna, Austria
| | - Adelheid Wöhrer
- Institute of Neurology, Medical University of Vienna, A-1090, Vienna, Austria
| | - Brendan D Price
- Department of Radiation Oncology, Division of Genomic Instability and DNA Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Bruce Demple
- Department of Pharmacological Sciences, Stony Brook University, School of Medicine, Stony Brook, NY, 11794-8651, USA
| | - Okay Saydam
- Molecular Neuro-Oncology Research Unit, Department of Pediatrics & Adolescent Medicine, Medical University of Vienna, A-1090, Vienna, Austria.,Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Nurten Saydam
- Molecular Neuro-Oncology Research Unit, Department of Pediatrics & Adolescent Medicine, Medical University of Vienna, A-1090, Vienna, Austria. .,Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA.
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34
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Chiang SC, Meagher M, Kassouf N, Hafezparast M, McKinnon PJ, Haywood R, El-Khamisy SF. Mitochondrial protein-linked DNA breaks perturb mitochondrial gene transcription and trigger free radical-induced DNA damage. SCIENCE ADVANCES 2017; 3:e1602506. [PMID: 28508041 PMCID: PMC5409496 DOI: 10.1126/sciadv.1602506] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 03/02/2017] [Indexed: 05/06/2023]
Abstract
Breakage of one strand of DNA is the most common form of DNA damage. Most damaged DNA termini require end-processing in preparation for ligation. The importance of this step is highlighted by the association of defects in the 3'-end processing enzyme tyrosyl DNA phosphodiesterase 1 (TDP1) and neurodegeneration and by the cytotoxic induction of protein-linked DNA breaks (PDBs) and oxidized nucleic acid intermediates during chemotherapy and radiotherapy. Although much is known about the repair of PDBs in the nucleus, little is known about this process in the mitochondria. We reveal that TDP1 resolves mitochondrial PDBs (mtPDBs), thereby promoting mitochondrial gene transcription. Overexpression of a toxic form of mitochondrial topoisomerase I (TOP1mt*), which generates excessive mtPDBs, results in a TDP1-dependent compensatory up-regulation of mitochondrial gene transcription. In the absence of TDP1, the imbalance in transcription of mitochondrial- and nuclear-encoded electron transport chain (ETC) subunits results in misassembly of ETC complex III. Bioenergetics profiling further reveals that TDP1 promotes oxidative phosphorylation under both basal and high energy demands. It is known that mitochondrial dysfunction results in free radical leakage and nuclear DNA damage; however, the detection of intermediates of radical damage to DNA is yet to be shown. Consequently, we report an increased accumulation of carbon-centered radicals in cells lacking TDP1, using electron spin resonance spectroscopy. Overexpression of the antioxidant enzyme superoxide dismutase 1 (SOD1) reduces carbon-centered adducts and protects TDP1-deficient cells from oxidative stress. Conversely, overexpression of the amyotrophic lateral sclerosis-associated mutant SOD1G93A leads to marked sensitivity. Whereas Tdp1 knockout mice develop normally, overexpression of SOD1G93A suggests early embryonic lethality. Together, our data show that TDP1 resolves mtPDBs, thereby regulating mitochondrial gene transcription and oxygen consumption by oxidative phosphorylation, thus conferring cellular protection against reactive oxygen species-induced damage.
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Affiliation(s)
- Shih-Chieh Chiang
- Krebs Institute and Sheffield Institute for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN Sheffield, U.K
| | - Martin Meagher
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K
| | - Nick Kassouf
- RAFT Institute, Mount Vernon Hospital, Northwood, Middlesex HA6 2RN, U.K
| | - Majid Hafezparast
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, U.K
| | - Peter J. McKinnon
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN 38105–3678, USA
| | - Rachel Haywood
- RAFT Institute, Mount Vernon Hospital, Northwood, Middlesex HA6 2RN, U.K
| | - Sherif F. El-Khamisy
- Krebs Institute and Sheffield Institute for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN Sheffield, U.K
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12588, Egypt
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35
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Personalised Medicine: Genome Maintenance Lessons Learned from Studies in Yeast as a Model Organism. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1007:157-178. [PMID: 28840557 DOI: 10.1007/978-3-319-60733-7_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Yeast research has been tremendously contributing to the understanding of a variety of molecular pathways due to the ease of its genetic manipulation, fast doubling time as well as being cost-effective. The understanding of these pathways did not only help scientists learn more about the cellular functions but also assisted in deciphering the genetic and cellular defects behind multiple diseases. Hence, yeast research not only opened the doors for transforming basic research into applied research, but also paved the roads for improving diagnosis and innovating personalized therapy of different diseases. In this chapter, we discuss how yeast research has contributed to understanding major genome maintenance pathways such as the S-phase checkpoint activation pathways, repair via homologous recombination and non-homologous end joining as well as topoisomerases-induced protein linked DNA breaks repair. Defects in these pathways lead to neurodegenerative diseases and cancer. Thus, the understanding of the exact genetic defects underlying these diseases allowed the development of personalized medicine, improving the diagnosis and treatment and overcoming the detriments of current conventional therapies such as the side effects, toxicity as well as drug resistance.
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36
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Allam WR, Ashour ME, Waly AA, El-Khamisy S. Role of Protein Linked DNA Breaks in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1007:41-58. [PMID: 28840551 DOI: 10.1007/978-3-319-60733-7_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Topoisomerases are a group of specialized enzymes that function to maintain DNA topology by introducing transient DNA breaks during transcription and replication. As a result of abortive topoisomerases activity, topoisomerases catalytic intermediates may be trapped on the DNA forming topoisomerase cleavage complexes (Topcc). Topoisomerases trapping on the DNA is the mode of action of several anticancer drugs, it lead to formation of protein linked DAN breaks (PDBs). PDBs are now considered as one of the most dangerous forms of endogenous DNA damage and a major threat to genomic stability. The repair of PDBs involves both the sensing and repair pathways. Unsuccessful repair of PDBs leads to different signs of genomic instabilities such as chromosomal rearrangements and cancer predisposition. In this chapter we will summarize the role of topoisomerases induced PDBs, identification and signaling, repair, role in transcription. We will also discuss the role of PDBs in cancer with a special focus on prostate cancer.
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Affiliation(s)
- Walaa R Allam
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.
| | - Mohamed E Ashour
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Amr A Waly
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Sherif El-Khamisy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt. .,Krebs Institute and Sheffield Institute for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, Sheffield, S10 2TN, UK.
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37
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Zakharenko A, Luzina O, Koval O, Nilov D, Gushchina I, Dyrkheeva N, Švedas V, Salakhutdinov N, Lavrik O. Tyrosyl-DNA Phosphodiesterase 1 Inhibitors: Usnic Acid Enamines Enhance the Cytotoxic Effect of Camptothecin. JOURNAL OF NATURAL PRODUCTS 2016; 79:2961-2967. [PMID: 27933897 DOI: 10.1021/acs.jnatprod.6b00979] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a repair enzyme for stalled DNA-topoisomerase 1 (Top1) cleavage complexes and other 3'-end DNA lesions. TDP1 is a perspective target for anticancer therapy based on Top1-poison-mediated DNA damage. Several novel usnic acid derivatives with an enamine moiety have been synthesized and tested as inhibitors of TDP1. The enamines of usnic acid showed IC50 values in the range of 0.16 to 2.0 μM. These compounds revealed moderate cytotoxicity against human tumor MCF-7 cells. These new compounds enhanced the cytotoxicity of the established Top1 poison camptothecin by an order of magnitude.
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Affiliation(s)
- Alexandra Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk, 630090, Russian Federation
| | - Olga Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences , Novosibirsk, 630090, Russian Federation
| | - Olga Koval
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk, 630090, Russian Federation
- Novosibirsk State University , Novosibirsk, 630090, Russian Federation
| | | | | | - Nadezhda Dyrkheeva
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk, 630090, Russian Federation
| | | | - Nariman Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences , Novosibirsk, 630090, Russian Federation
- Novosibirsk State University , Novosibirsk, 630090, Russian Federation
| | - Olga Lavrik
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk, 630090, Russian Federation
- Novosibirsk State University , Novosibirsk, 630090, Russian Federation
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38
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Laev SS, Salakhutdinov NF, Lavrik OI. Tyrosyl-DNA phosphodiesterase inhibitors: Progress and potential. Bioorg Med Chem 2016; 24:5017-5027. [PMID: 27687971 DOI: 10.1016/j.bmc.2016.09.045] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/30/2016] [Accepted: 09/18/2016] [Indexed: 10/21/2022]
Abstract
DNA topoisomerases are essential during transcription and replication. The therapeutic mechanism of action of topoisomerase inhibitors is enzyme poisoning rather than catalytic inhibition. Tyrosyl-DNA phosphodiesterases 1 or 2 were found as DNA repair enzymes hydrolyzing the covalent bond between the tyrosyl residue of topoisomerases I or II and the 3'- or 5'-phosphate groups in DNA, respectively. Tyrosyl-DNA phosphodiesterase 1 is a key enzyme in DNA repair machinery and a promising target for antitumor and neurodegenerative therapy. Inhibitors of tyrosyl-DNA phosphodiesterase 1 could act synergistically with topoisomerase I inhibitors and thereby potentiate the effects of topoisomerase I poisons. Tyrosyl-DNA phosphodiesterase 2 is an enzyme that specifically repairs DNA damages induced by topoisomerase II poisons and causes resistance to these drugs. Selective inhibition of tyrosyl-DNA phosphodiesterase 2 may be a novel approach to overcome intrinsic or acquired resistance to topoisomerase II-targeted drug therapy. Thus, agents that inhibit tyrosyl-DNA phosphodiesterases 1 and 2 have many applications in biochemical and physiological research and they have the potential to become anticancer and antiviral drugs. The structures, mechanism of action and therapeutic rationale of tyrosyl-DNA phosphodiesterase inhibitors and their development for combinations with topoisomerase inhibitors and DNA damaging agents are discussed.
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Affiliation(s)
- Sergey S Laev
- Vorozhtsov Institute of Organic Chemistry, Siberian Division, Russian Academy of Sciences, pr. akademika Lavrent'eva 9, Novosibirsk 630090, Russian Federation.
| | - Nariman F Salakhutdinov
- Vorozhtsov Institute of Organic Chemistry, Siberian Division, Russian Academy of Sciences, pr. akademika Lavrent'eva 9, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russian Federation
| | - Olga I Lavrik
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russian Federation; Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Division, Russian Academy of Sciences, pr. akademika Lavrent'eva 8, Novosibirsk 630090, Russian Federation
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39
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Lee YR, Kim KM, Jeon BH, Choi S. Extracellularly secreted APE1/Ref-1 triggers apoptosis in triple-negative breast cancer cells via RAGE binding, which is mediated through acetylation. Oncotarget 2016; 6:23383-98. [PMID: 26125438 PMCID: PMC4695125 DOI: 10.18632/oncotarget.4345] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/12/2015] [Indexed: 12/31/2022] Open
Abstract
The present study evaluated the mechanism of apoptosis caused by post-translational modification, hyperacetylation in triple-negative breast cancer (TNBC) cells. We previously showed that trichostatin A (TSA) induced secretion of acetylated apurinic apyrimidinic endonuclease 1/redox factor-1 (Ac-APE1/Ref-1). This is the first report showing that Ac-APE1/Ref-1 initiates apoptosis in TNBC cells by binding to the receptor for advanced glycation end products (RAGE). The functional significance of secreted Ac-APE1/Ref-1 was studied by induction of intracellular hyperacetylation through co-treatment with acetylsalicylic acid and TSA in MDA-MB-231 cells. In response to hyperacetylation, secretion of Ac-APE1/Ref-1 in vesicles was observed, resulting in significantly decreased cell viability and induction of apoptosis with increased expression of RAGE. The hyperacetylation-induced apoptosis was similar in two other TNBC cell lines: BT-459 and MDA-MB-468. Therefore, hyperacetylation may be a therapeutic target for treatment of TNBCs. This study introduces a novel paradigm whereby post-translational modification induces apoptotic cell death in breast cancer cells resistant to standard chemotherapeutic agents through secretion of auto- or paracrine molecules such as Ac-APE1/Ref-1.
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Affiliation(s)
- Yu Ran Lee
- Research Institute of Medical Sciences, Department of Physiology, School of Medicine, Chungnam National University, Daejeon, 301747, Korea
| | - Ki Mo Kim
- Cancer Research Team, Korean Medicine Based Herbal Drug Research Group, Herbal Medicine Research Division, Korea Institute of Oriental Medicine, (KIOM), Daejeon, 305811, Korea
| | - Byeong Hwa Jeon
- Research Institute of Medical Sciences, Department of Physiology, School of Medicine, Chungnam National University, Daejeon, 301747, Korea
| | - Sunga Choi
- Research Institute of Medical Sciences, Department of Physiology, School of Medicine, Chungnam National University, Daejeon, 301747, Korea
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40
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End-processing nucleases and phosphodiesterases: An elite supporting cast for the non-homologous end joining pathway of DNA double-strand break repair. DNA Repair (Amst) 2016; 43:57-68. [PMID: 27262532 DOI: 10.1016/j.dnarep.2016.05.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/05/2016] [Indexed: 11/20/2022]
Abstract
Nonhomologous end joining (NHEJ) is an error-prone DNA double-strand break repair pathway that is active throughout the cell cycle. A substantial fraction of NHEJ repair events show deletions and, less often, insertions in the repair joints, suggesting an end-processing step comprising the removal of mismatched or damaged nucleotides by nucleases and other phosphodiesterases, as well as subsequent strand extension by polymerases. A wide range of nucleases, including Artemis, Metnase, APLF, Mre11, CtIP, APE1, APE2 and WRN, are biochemically competent to carry out such double-strand break end processing, and have been implicated in NHEJ by at least circumstantial evidence. Several additional DNA end-specific phosphodiesterases, including TDP1, TDP2 and aprataxin are available to resolve various non-nucleotide moieties at DSB ends. This review summarizes the biochemical specificities of these enzymes and the evidence for their participation in the NHEJ pathway.
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41
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Cristini A, Park JH, Capranico G, Legube G, Favre G, Sordet O. DNA-PK triggers histone ubiquitination and signaling in response to DNA double-strand breaks produced during the repair of transcription-blocking topoisomerase I lesions. Nucleic Acids Res 2016; 44:1161-78. [PMID: 26578593 PMCID: PMC4756817 DOI: 10.1093/nar/gkv1196] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/23/2015] [Accepted: 10/26/2015] [Indexed: 12/12/2022] Open
Abstract
Although defective repair of DNA double-strand breaks (DSBs) leads to neurodegenerative diseases, the processes underlying their production and signaling in non-replicating cells are largely unknown. Stabilized topoisomerase I cleavage complexes (Top1cc) by natural compounds or common DNA alterations are transcription-blocking lesions whose repair depends primarily on Top1 proteolysis and excision by tyrosyl-DNA phosphodiesterase-1 (TDP1). We previously reported that stabilized Top1cc produce transcription-dependent DSBs that activate ATM in neurons. Here, we use camptothecin (CPT)-treated serum-starved quiescent cells to induce transcription-blocking Top1cc and show that those DSBs are generated during Top1cc repair from Top1 peptide-linked DNA single-strand breaks generated after Top1 proteolysis and before excision by TDP1. Following DSB induction, ATM activates DNA-PK whose inhibition suppresses H2AX and H2A ubiquitination and the later assembly of activated ATM into nuclear foci. Inhibition of DNA-PK also reduces Top1 ubiquitination and proteolysis as well as resumption of RNA synthesis suggesting that DSB signaling further enhances Top1cc repair. Finally, we show that co-transcriptional DSBs kill quiescent cells. Together, these new findings reveal that DSB production and signaling by transcription-blocking Top1 lesions impact on non-replicating cell fate and provide insights on the molecular pathogenesis of neurodegenerative diseases such as SCAN1 and AT syndromes, which are caused by TDP1 and ATM deficiency, respectively.
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Affiliation(s)
- Agnese Cristini
- Cancer Research Center of Toulouse, INSERM UMR1037, Toulouse 31037, France
| | - Joon-Hyung Park
- Cancer Research Center of Toulouse, INSERM UMR1037, Toulouse 31037, France
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Gaëlle Legube
- Université de Toulouse, UPS, LBCMCP, 31062 Toulouse, France CNRS, LBCMCP, 31062 Toulouse, France
| | - Gilles Favre
- Cancer Research Center of Toulouse, INSERM UMR1037, Toulouse 31037, France
| | - Olivier Sordet
- Cancer Research Center of Toulouse, INSERM UMR1037, Toulouse 31037, France
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Borda MA, Palmitelli M, Verón G, González-Cid M, de Campos Nebel M. Tyrosyl-DNA-phosphodiesterase I (TDP1) participates in the removal and repair of stabilized-Top2α cleavage complexes in human cells. Mutat Res 2015; 781:37-48. [PMID: 26421495 DOI: 10.1016/j.mrfmmm.2015.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 08/21/2015] [Accepted: 09/11/2015] [Indexed: 02/01/2023]
Abstract
Tyrosyl-DNA-phosphodiesterase 1 (TDP1) is a DNA repair enzyme that removes irreversible protein-linked 3' DNA complexes, 3' phosphoglycolates, alkylation damage-induced DNA breaks, and 3' deoxyribose nucleosides. In addition to its extended spectrum of substrates, TDP1 interacts with several DNA damage response factors. To determine whether TDP1 participates in the repair of topoisomerase II (Top2) induced DNA lesions, we generated TDP1 depleted (TDP1kd) human tumoral cells. We found that TDP1kd cells are hypersensitive to etoposide (ETO). Moreover, we established in a chromatin context that following treatment with ETO, TDP1kd cells accumulate increased amounts of Top2α cleavage complexes, removing them with an altered kinetics. We also showed that TDP1 depleted cells accumulate increased γH2AX and pS296Chk1 signals following treatment with ETO. Similarly, cytogenetics analyses following Top2 poisoning revealed increased amounts of chromatid and chromosome breaks and exchanges on TDP1kd cells in the presence or not of the DNA-PKcs inhibitor NU7026. However, the levels of sister chromatid exchanges were similar in both TDP1kd and control non-silenced cell lines. This suggests a role of TDP1 in both canonical non-homologous end joining and alternative end joining, but not in the homologous recombination repair pathway. Finally, micronucleus analyses following ETO treatment revealed a higher frequency of micronucleus containing γH2AX signals on TDP1kd cells. Together, our results highlight an active role of TDP1 in the repair of Top2-induced DNA damage and its relevance on the genome stability maintenance in human cells.
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Affiliation(s)
- Miguel Angel Borda
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (CONICET-Academia Nacional de Medicina), Buenos Aires, Argentina
| | - Micaela Palmitelli
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (CONICET-Academia Nacional de Medicina), Buenos Aires, Argentina
| | - Gustavo Verón
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (CONICET-Academia Nacional de Medicina), Buenos Aires, Argentina
| | - Marcela González-Cid
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (CONICET-Academia Nacional de Medicina), Buenos Aires, Argentina
| | - Marcelo de Campos Nebel
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (CONICET-Academia Nacional de Medicina), Buenos Aires, Argentina.
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43
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Heo J, Li J, Summerlin M, Hays A, Katyal S, McKinnon PJ, Nitiss KC, Nitiss JL, Hanakahi LA. TDP1 promotes assembly of non-homologous end joining protein complexes on DNA. DNA Repair (Amst) 2015; 30:28-37. [PMID: 25841101 DOI: 10.1016/j.dnarep.2015.03.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 02/25/2015] [Accepted: 03/09/2015] [Indexed: 11/16/2022]
Abstract
The repair of DNA double-strand breaks (DSB) is central to the maintenance of genomic integrity. In tumor cells, the ability to repair DSBs predicts response to radiation and many cytotoxic anti-cancer drugs. DSB repair pathways include homologous recombination and non-homologous end joining (NHEJ). NHEJ is a template-independent mechanism, yet many NHEJ repair products carry limited genetic changes, which suggests that NHEJ includes mechanisms to minimize error. Proteins required for mammalian NHEJ include Ku70/80, the DNA-dependent protein kinase (DNA-PKcs), XLF/Cernunnos and the XRCC4:DNA ligase IV complex. NHEJ also utilizes accessory proteins that include DNA polymerases, nucleases, and other end-processing factors. In yeast, mutations of tyrosyl-DNA phosphodiesterase (TDP1) reduced NHEJ fidelity. TDP1 plays an important role in repair of topoisomerase-mediated DNA damage and 3'-blocking DNA lesions, and mutation of the human TDP1 gene results in an inherited human neuropathy termed SCAN1. We found that human TDP1 stimulated DNA binding by XLF and physically interacted with XLF to form TDP1:XLF:DNA complexes. TDP1:XLF interactions preferentially stimulated TDP1 activity on dsDNA as compared to ssDNA. TDP1 also promoted DNA binding by Ku70/80 and stimulated DNA-PK activity. Because Ku70/80 and XLF are the first factors recruited to the DSB at the onset of NHEJ, our data suggest a role for TDP1 during the early stages of mammalian NHEJ.
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Affiliation(s)
- Jinho Heo
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - Jing Li
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - Matthew Summerlin
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - Annette Hays
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - Sachin Katyal
- University of Manitoba, Department of Pharmacology and Therapeutics, Manitoba Institute of Cell Biology, 675 McDermot Avenue, Winnipeg, Manitoba, Canada R3E 0V9
| | - Peter J McKinnon
- Department of Genetics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Karin C Nitiss
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - John L Nitiss
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - Leslyn A Hanakahi
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA; Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA.
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44
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Zakharenko A, Khomenko T, Zhukova S, Koval O, Zakharova O, Anarbaev R, Lebedeva N, Korchagina D, Komarova N, Vasiliev V, Reynisson J, Volcho K, Salakhutdinov N, Lavrik O. Synthesis and biological evaluation of novel tyrosyl-DNA phosphodiesterase 1 inhibitors with a benzopentathiepine moiety. Bioorg Med Chem 2015; 23:2044-52. [PMID: 25819333 DOI: 10.1016/j.bmc.2015.03.020] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Revised: 03/02/2015] [Accepted: 03/05/2015] [Indexed: 01/28/2023]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a promising target for antitumor therapy based on Top1 poison-mediated DNA damage. Several novel benzopentathiepines were synthesized and tested as inhibitors of TDP1 using a new oligonucleotide-based fluorescence assay. The benzopentathiepines have IC₅₀ values in the range of 0.2-6.0 μM. According to the molecular modeling, the conformational flexibility of the dibutylamine group of the most effective inhibitor (3d) allows it to occupy an advantageous position for effective binding compared to its cyclic counterparts. The study of cytotoxicity of these compounds revealed that all compounds cause an apoptotic cell death in MCF-7 and Hep G2 cells. Therefore the new class of very effective inhibitors of TDP1 was elaborated.
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Affiliation(s)
- Alexandra Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation
| | - Tatyana Khomenko
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - Svetlana Zhukova
- Altai State University, 61, Lenina Ave., Barnaul 656049, Russian Federation
| | - Olga Koval
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - Olga Zakharova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation
| | - Rashid Anarbaev
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - Natalya Lebedeva
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - Dina Korchagina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation
| | - Nina Komarova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation
| | - Vladimir Vasiliev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation
| | | | - Konstantin Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - Nariman Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation.
| | - Olga Lavrik
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation.
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45
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Ashour ME, Atteya R, El-Khamisy SF. Topoisomerase-mediated chromosomal break repair: an emerging player in many games. Nat Rev Cancer 2015; 15:137-51. [PMID: 25693836 DOI: 10.1038/nrc3892] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The mammalian genome is constantly challenged by exogenous and endogenous threats. Although much is known about the mechanisms that maintain DNA and RNA integrity, we know surprisingly little about the mechanisms that underpin the pathology and tissue specificity of many disorders caused by defective responses to DNA or RNA damage. Of the different types of endogenous damage, protein-linked DNA breaks (PDBs) are emerging as an important player in cancer development and therapy. PDBs can arise during the abortive activity of DNA topoisomerases, a class of enzymes that modulate DNA topology during several chromosomal transactions, such as gene transcription and DNA replication, recombination and repair. In this Review, we discuss the mechanisms underpinning topoisomerase-induced PDB formation and repair with a focus on their role during gene transcription and the development of tissue-specific cancers.
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Affiliation(s)
- Mohamed E Ashour
- 1] Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK. [2] Center for Genomics, Helmy Institute, Zewail City of Science and Technology, Giza 12588, Egypt
| | - Reham Atteya
- Center for Genomics, Helmy Institute, Zewail City of Science and Technology, Giza 12588, Egypt
| | - Sherif F El-Khamisy
- 1] Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK. [2] Center for Genomics, Helmy Institute, Zewail City of Science and Technology, Giza 12588, Egypt
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46
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Meisenberg C, Gilbert DC, Chalmers A, Haley V, Gollins S, Ward SE, El-Khamisy SF. Clinical and cellular roles for TDP1 and TOP1 in modulating colorectal cancer response to irinotecan. Mol Cancer Ther 2015; 14:575-85. [PMID: 25522766 PMCID: PMC4340569 DOI: 10.1158/1535-7163.mct-14-0762] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Colorectal cancer is the third most common cancer in the world. Despite surgery, up to 50% of patients relapse with incurable disease. First-line chemotherapy uses the topoisomerase 1 (TOP1) poison irinotecan, which triggers cell death by trapping TOP1 on DNA. The removal of TOP1 peptide from TOP1-DNA breaks is conducted by tyrosyl-DNA phosphodiesterase 1 (TDP1). Despite putative roles for TDP1 and TOP1 in colorectal cancer, their role in cellular and clinical responses to TOP1-targeting therapies remains unclear. Here, we show varying expression levels of TOP1 and TDP1 polypeptides in multiple colorectal cancer cell lines and in clinical colorectal cancer samples. TDP1 overexpression or TOP1 depletion is protective. Conversely, TDP1 depletion increases DNA-strand breakage and hypersensitivity to irinotecan in a TOP1-dependent manner, presenting a potential therapeutic opportunity in colorectal cancer. TDP1 protein levels correlate well with mRNA and with TDP1 catalytic activity. However, no correlation is observed between inherent TDP1 or TOP1 levels alone and irinotecan sensitivity, pointing at their limited utility as predictive biomarkers in colorectal cancer. These findings establish TDP1 as a potential therapeutic target for the treatment of colorectal cancer and question the validity of TOP1 or TDP1 on their own as predictive biomarkers for irinotecan response.
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Affiliation(s)
- Cornelia Meisenberg
- The Wellcome Trust DNA Repair Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Duncan C Gilbert
- Sussex Cancer Centre, Royal Sussex County Hospital, Brighton, United Kingdom
| | - Anthony Chalmers
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Vikki Haley
- Faculty of Science, Department of Life, Health and Chemical Sciences, The Open University, Milton Keynes, United Kingdom
| | - Simon Gollins
- North Wales Cancer Treatment Centre, Betsi Cadwaladr University of Health Board, Ysbty Glan Clwyd, Bodelwyddan, Rhyl, United Kingdom
| | - Simon E Ward
- Translational Drug Discovery Group, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sherif F El-Khamisy
- The Wellcome Trust DNA Repair Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom. Mammalian Genome Stability Group, Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom. Center of Genomics, Helmy Institute, Zewail City of Science and Technology, Giza, Egypt.
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47
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Arabshahi HJ, van Rensburg M, Pilkington LI, Jeon CY, Song M, Gridel LM, Leung E, Barker D, Vuica-Ross M, Volcho KP, Zakharenko AL, Lavrik OI, Reynisson J. A synthesis, in silico, in vitro and in vivo study of thieno[2,3-b]pyridine anticancer analogues. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00245a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The thieno[2,3-b]pyridines bind to TDP1 with the best analogue 9d with IC50 at 0.5 μM.
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Affiliation(s)
| | | | - Lisa I. Pilkington
- School of Chemical Sciences
- University of Auckland
- Auckland 1142
- New Zealand
- Auckland Cancer Society Research Centre and Department of Molecular Medicine and Pathology
| | - Chae Yeon Jeon
- School of Chemical Sciences
- University of Auckland
- Auckland 1142
- New Zealand
| | - Mirae Song
- School of Chemical Sciences
- University of Auckland
- Auckland 1142
- New Zealand
| | - Ling-Mey Gridel
- School of Chemical Sciences
- University of Auckland
- Auckland 1142
- New Zealand
| | - Euphemia Leung
- Auckland Cancer Society Research Centre and Department of Molecular Medicine and Pathology
- University of Auckland
- New Zealand
| | - David Barker
- School of Chemical Sciences
- University of Auckland
- Auckland 1142
- New Zealand
| | | | - Konstantin P. Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry
- Siberian Branch of the Russian Academy of Sciences
- Novosibirsk
- Russian Federation
- Novosibirsk State University
| | - Alexandra L. Zakharenko
- Institute of Chemical Biology and Fundamental Medicine
- Siberian Branch of the Russian Academy of Sciences
- Novosibirsk
- Russian Federation
| | - Olga I. Lavrik
- Novosibirsk State University
- Novosibirsk
- Russian Federation
- Institute of Chemical Biology and Fundamental Medicine
- Siberian Branch of the Russian Academy of Sciences
| | - Jóhannes Reynisson
- School of Chemical Sciences
- University of Auckland
- Auckland 1142
- New Zealand
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48
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Neuroprotection and repair of 3'-blocking DNA ends by glaikit (gkt) encoding Drosophila tyrosyl-DNA phosphodiesterase 1 (TDP1). Proc Natl Acad Sci U S A 2014; 111:15816-20. [PMID: 25331878 DOI: 10.1073/pnas.1415011111] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Tyrosyl-DNA phosphodiesterase (TDP1) is a phylogenetically conserved enzyme critical for the removal of blocking lesions at the 3' ends of DNA or RNA. This study analyzes the Drosophila TDP1 gene ortholog glaikit (gkt) and its possible role(s) in the repair of endogenous DNA lesions and neuroprotection. To do so, we studied a homozygous PiggyBac insertion (c03958) that disrupts the 5' UTR of gkt. Protein extracts of c03958 flies were defective in hydrolyzing 3'-DNA-tyrosyl residues, demonstrating that gkt is the Drosophila TDP1. Although the mutant is generally healthy and fertile, females exhibit reduced lifespan and diminished climbing ability. This phenotype was rescued by neuronal expression of TDP1. In addition, when c03958 larvae were exposed to bleomycin, an agent that produces oxidative DNA damage, or topoisomerase I-targeted drugs (camptothecin and a noncamptothecin indenoisoquinoline derivative, LMP-776), survivors displayed rough eye patches, which were rescued by neuronal expression of TDP1. Our study establishes that gkt is the Drosophila TDP1 gene, and that it is critical for neuroprotection, normal longevity, and repair of damaged DNA.
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49
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Comeaux EQ, van Waardenburg RCAM. Tyrosyl-DNA phosphodiesterase I resolves both naturally and chemically induced DNA adducts and its potential as a therapeutic target. Drug Metab Rev 2014; 46:494-507. [PMID: 25327705 DOI: 10.3109/03602532.2014.971957] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA is subject to a wide range of insults, resulting from endogenous and exogenous sources that need to be metabolized/resolved to maintain genome integrity. Tyrosyl-DNA phosphodiesterase I (Tdp1) is a eukaryotic DNA repair enzyme that catalyzes the removal of covalent 3'-DNA adducts. As a phospholipase D superfamily member Tdp1 utilizes two catalytic histidines each within a His-Lys-Asn motif. Tdp1 was discovered for its ability to hydrolyze the 3'-phospho-tyrosyl that in the cell covalently links DNA Topoisomerase I (Topo1) and DNA. Tdp1's list of substrates has since grown and can be divided into two groups: protein-DNA adducts, such as camptothecin stabilized Topo1-DNA adducts, and modified nucleotides, including oxidized nucleotides and chain terminating nucleoside analogs. Since many of Tdp1's substrates are generated by clinically relevant chemotherapeutics, Tdp1 became a therapeutic target for molecularly targeted small molecules. Tdp1's unique catalytic cycle allows for two different targeting strategies: (1) the intuitive inhibition of Tdp1 catalysis to prevent Tdp1-mediated repair of chemotherapeutically induced DNA adducts, thereby enhancing their toxicity and (2) stabilization of the Tdp1-DNA covalent reaction intermediate, prevents resolution of Tdp1-DNA adduct and increases the half-life of this potentially toxic DNA adduct. This concept is best illustrated by a catalytic Tdp1 mutant that forms the molecular basis of the autosomal recessive neurodegenerative disease spinocerebellar ataxia with axonal neuropathy, and results in an increased stability of its Tdp1-DNA reaction intermediate. Here, we will discuss Tdp1 catalysis from a structure-function perspective, Tdp1 substrates and Tdp1 potential as a therapeutic target.
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Affiliation(s)
- Evan Q Comeaux
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham , Birmingham, AL , USA
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50
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Meisenberg C, Ward SE, Schmid P, El-Khamisy SF. TDP1/TOP1 Ratio as a Promising Indicator for the Response of Small Cell Lung Cancer to Topotecan. JOURNAL OF CANCER SCIENCE & THERAPY 2014; 6:258-267. [PMID: 25232464 PMCID: PMC4163653 DOI: 10.4172/1948-5956.1000280] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND AND OBJECTIVE Small cell lung cancer (SCLC) is one of the most challenging tumors to treat due to high proliferation rate, early metastatic dissemination and rapid development of chemotherapy resistance. The current treatment protocols involve the use of topoisomerase 1 (TOP1) poisons such as irinotecan and topotecan in combination with platinum-based compounds. TOP1 poisons kill cancer cells by trapping TOP1 on DNA, generating lethal DNA double-strand breaks. A potential mechanism employed by cancer cells to resist killing by TOP1 poisons is to overexpress enzymes involved in the repair of TOP1-DNA breaks. Tyrosyl DNA phosphodiesterase 1 (TDP1) is a key player in this process and despite its importance, no data is currently available to correlate TDP1 protein and mRNA levels with catalytic activity in SCLC. In addition, it is not known if TDP1 and TOP1 protein levels correlate with the cellular response of SCLC to TOP1 based therapies. METHODS AND RESULTS We report a remarkable variation in TDP1 and TOP1 protein levels in a panel of SCLC cell lines. TDP1 protein level correlates well with TDP1 mRNA and TDP1 catalytic activity, as measured by two newly developed independent activity assays, suggesting the potential utility of immunohistochemistry in assessing TDP1 levels in SCLC tissues. We further demonstrate that whilst TDP1 protein level alone does not correlate with topotecan sensitivity, TDP1/TOP1 ratio correlates well with sensitivity in 8 out of 10 cell lines examined. CONCLUSION This study provides the first cellular analyses of TDP1 and TOP1 in SCLC and suggests the potential utility of TDP1/TOP1 ratio to assess the response of SCLC to topotecan. The establishment and validation of an easy-to-use TDP1 enzymatic assay in cell extracts could be exploited as a diagnostic tool in the clinic. These findings may help in stratifying patients that are likely to benefit from TOP1 poisons and TDP1 inhibitors currently under development.
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Affiliation(s)
- Cornelia Meisenberg
- The Wellcome Trust DNA Repair Group, Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Simon E Ward
- The Sussex Translational Drug Discovery Group, University of Sussex, Brighton, UK
| | - Peter Schmid
- Brighton and Sussex Medical School, University of Sussex, Brighton, UK (former affiliation)
- Centre of Experimental Cancer Medicine, Barts Cancer Institute, Queen Mary University London, UK
| | - Sherif F El-Khamisy
- The Wellcome Trust DNA Repair Group, Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
- Center of Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
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