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Pagano P, Pagano A, Paternolli S, Balestrazzi A, Macovei A. Integrative Transcriptomics Data Mining to Explore the Functions of TDP1α and TDP1β Genes in the Arabidopsis thaliana Model Plant. Genes (Basel) 2023; 14:genes14040884. [PMID: 37107642 PMCID: PMC10137840 DOI: 10.3390/genes14040884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
The tyrosyl-DNA phosphodiesterase 1 (TDP1) enzyme hydrolyzes the phosphodiester bond between a tyrosine residue and the 3'-phosphate of DNA in the DNA-topoisomerase I (TopI) complex, being involved in different DNA repair pathways. A small TDP1 gene subfamily is present in plants, where TDP1α has been linked to genome stability maintenance, while TDP1β has unknown functions. This work aimed to comparatively investigate the function of the TDP1 genes by taking advantage of the rich transcriptomics databases available for the Arabidopsis thaliana model plant. A data mining approach was carried out to collect information regarding gene expression in different tissues, genetic backgrounds, and stress conditions, using platforms where RNA-seq and microarray data are deposited. The gathered data allowed us to distinguish between common and divergent functions of the two genes. Namely, TDP1β seems to be involved in root development and associated with gibberellin and brassinosteroid phytohormones, whereas TDP1α is more responsive to light and abscisic acid. During stress conditions, both genes are highly responsive to biotic and abiotic treatments in a time- and stress-dependent manner. Data validation using gamma-ray treatments applied to Arabidopsis seedlings indicated the accumulation of DNA damage and extensive cell death associated with the observed changes in the TDP1 genes expression profiles.
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Affiliation(s)
- Paola Pagano
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Andrea Pagano
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Stefano Paternolli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
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2
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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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3
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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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4
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Byun JS, Park S, Yi DI, Shin JH, Hernandez SG, Hewitt SM, Nicklaus MC, Peach ML, Guasch L, Tang B, Wakefield LM, Yan T, Caban A, Jones A, Kabbout M, Vohra N, Nápoles AM, Singhal S, Yancey R, De Siervi A, Gardner K. Epigenetic re-wiring of breast cancer by pharmacological targeting of C-terminal binding protein. Cell Death Dis 2019; 10:689. [PMID: 31534138 PMCID: PMC6751206 DOI: 10.1038/s41419-019-1892-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/17/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023]
Abstract
The C-terminal binding protein (CtBP) is an NADH-dependent dimeric family of nuclear proteins that scaffold interactions between transcriptional regulators and chromatin-modifying complexes. Its association with poor survival in several cancers implicates CtBP as a promising target for pharmacological intervention. We employed computer-assisted drug design to search for CtBP inhibitors, using quantitative structure-activity relationship (QSAR) modeling and docking. Functional screening of these drugs identified 4 compounds with low toxicity and high water solubility. Micro molar concentrations of these CtBP inhibitors produces significant de-repression of epigenetically silenced pro-epithelial genes, preferentially in the triple-negative breast cancer cell line MDA-MB-231. This epigenetic reprogramming occurs through eviction of CtBP from gene promoters; disrupted recruitment of chromatin-modifying protein complexes containing LSD1, and HDAC1; and re-wiring of activating histone marks at targeted genes. In functional assays, CtBP inhibition disrupts CtBP dimerization, decreases cell migration, abolishes cellular invasion, and improves DNA repair. Combinatorial use of CtBP inhibitors with the LSD1 inhibitor pargyline has synergistic influence. Finally, integrated correlation of gene expression in breast cancer patients with nuclear levels of CtBP1 and LSD1, reveals new potential therapeutic vulnerabilities. These findings implicate a broad role for this class of compounds in strategies for epigenetically targeted therapeutic intervention.
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Affiliation(s)
- Jung S Byun
- National Institute on Minority Health and Health Disparities, Bethesda, MD, 20892, USA
| | - Samson Park
- Genetics Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Dae Ik Yi
- Genetics Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Jee-Hye Shin
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | | | - Stephen M Hewitt
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 20892, USA
| | - Megan L Peach
- Basic Science Program, Chemical Biology Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Laura Guasch
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 20892, USA
| | - Binwu Tang
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Lalage M Wakefield
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Tingfen Yan
- National Human Genome Institute, Bethesda, MD, 20892, USA
| | - Ambar Caban
- National Institute on Minority Health and Health Disparities, Bethesda, MD, 20892, USA
| | - Alana Jones
- National Institute on Minority Health and Health Disparities, Bethesda, MD, 20892, USA
| | - Mohamed Kabbout
- National Institute on Minority Health and Health Disparities, Bethesda, MD, 20892, USA
| | - Nasreen Vohra
- Brody School of Medicine at East Carolina University, Greenville, NC, 27834, USA
| | - Anna María Nápoles
- National Institute on Minority Health and Health Disparities, Bethesda, MD, 20892, USA
| | - Sandeep Singhal
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Ryan Yancey
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Adriana De Siervi
- Laboratorio de Oncologıa Molecular y Nuevos Blancos Terapeuticos, Instituto de Biologıa y Medicina Experimental (IBYME), CONICET, Buenos Aires, Argentina
| | - Kevin Gardner
- National Institute on Minority Health and Health Disparities, Bethesda, MD, 20892, USA. .,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA.
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5
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The Development of Tyrosyl-DNA Phosphodiesterase 1 Inhibitors. Combination of Monoterpene and Adamantine Moieties via Amide or Thioamide Bridges. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9132767] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Eleven amide and thioamide derivatives with monoterpene and adamantine substituents were synthesised. They were tested for their activity against the tyrosyl-DNA phosphodiesterase 1 DNA (Tdp1) repair enzyme with the most potent compound 47a, having an IC50 value of 0.64 M. When tested in the A-549 lung adenocarcinoma cell line, no or very limited cytotoxic effect was observed for the ligands. However, in conjunction with topotecan, a well-established Topoisomerase 1 (Top1) poison in clinical use against cancer, derivative 46a was very cytotoxic at 5 M concentration, displaying strong synergism. This effect was only seen for 46a (IC50—3.3 M) albeit some other ligands had better IC50 values. Molecular modelling into the catalytic site of Tdp1 predicted plausible binding mode of 46a, effectively blocking access to the catalytic site.
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Zakharenko A, Dyrkheeva N, Lavrik O. Dual DNA topoisomerase 1 and tyrosyl-DNA phosphodiesterase 1 inhibition for improved anticancer activity. Med Res Rev 2019; 39:1427-1441. [PMID: 31004352 DOI: 10.1002/med.21587] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 03/26/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a DNA repair enzyme that catalyzes the hydrolysis of the phosphodiester bond in the DNA-topoisomerase 1 (Top1) covalent complex and repairs some other 3'-end DNA adducts. Currently, Tdp1 functions as an important target in cancer drug design owing to its ability to break down various DNA adducts induced by chemotherapeutics. Tdp1 inhibitors may sensitize tumor cells to the action of Top1 poisons, thereby potentiating their effects. This mini-review summarizes findings from studies reporting the combined inhibition of Top1 and Tdp1. Two different approaches have been considered for developing such drug precursors.
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Affiliation(s)
- Alexandra Zakharenko
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Nadezhda Dyrkheeva
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Olga Lavrik
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russian Federation
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7
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Zakharova O, Luzina O, Zakharenko A, Sokolov D, Filimonov A, Dyrkheeva N, Chepanova A, Ilina E, Ilyina A, Klabenkova K, Chelobanov B, Stetsenko D, Zafar A, Eurtivong C, Reynisson J, Volcho K, Salakhutdinov N, Lavrik O. Synthesis and evaluation of aryliden- and hetarylidenfuranone derivatives of usnic acid as highly potent Tdp1 inhibitors. Bioorg Med Chem 2018; 26:4470-4480. [PMID: 30076000 DOI: 10.1016/j.bmc.2018.07.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 07/19/2018] [Accepted: 07/22/2018] [Indexed: 10/28/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a repair enzyme for stalled DNA-topoisomerase 1 (Top 1) cleavage complexes and other 3'-end DNA lesions. Tdp1 is a promising target for anticancer therapy, since it can repair DNA lesions caused by Top1 inhibitors leading to drug resistance. Hence, Tdp1 inhibition should result in synergistic effect with Top1 inhibitors. Twenty nine derivatives of (+)-usnic acid were tested for in vitro Tdp1 inhibitory activity using a fluorescent-based assay. Excellent activity was obtained, with derivative 6m demonstrating the lowest IC50 value of 25 nM. The established efficacy was verified using a gel-based assay, which gave close results to that of the fluorescent assay. In addition, molecular modeling in the Tdp1 substrate binding pocket suggested plausible binding modes for the active analogues. The synergistic effect of the Tdp1 inhibitors with topotecan, a Top1 poison in clinical use, was tested in two human cell lines, A-549 and HEK-293. Compounds 6k and 6x gave very promising results. In particular, 6x has a low cytotoxicity and an IC50 value of 63 nM, making it a valuable lead compound for the development of potent Tdp1 inhibitors for clinical use.
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Affiliation(s)
- Olga Zakharova
- 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
| | - Alexandra Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Dmitry Sokolov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Alexandr Filimonov
- 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
| | - Nadezhda Dyrkheeva
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Arina Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Ekaterina Ilina
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Anna Ilyina
- Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | | | - Boris Chelobanov
- 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
| | - Dmitry Stetsenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Ayesha Zafar
- School of Chemical Sciences, University of Auckland, New Zealand
| | | | | | - Konstantin Volcho
- 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
| | - 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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8
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Macovei A, Pagano A, Sabatini ME, Grandi S, Balestrazzi A. The Human Tyrosyl-DNA Phosphodiesterase 1 (hTdp1) Inhibitor NSC120686 as an Exploratory Tool to Investigate Plant Tdp1 Genes. Genes (Basel) 2018; 9:genes9040186. [PMID: 29597329 PMCID: PMC5924528 DOI: 10.3390/genes9040186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/16/2018] [Accepted: 03/23/2018] [Indexed: 11/21/2022] Open
Abstract
The hTdp1 (human tyrosyl-DNA phosphodiesterase 1) inhibitor NSC120686 has been used, along with topoisomerase inhibitors, as a pharmacophoric model to restrain the Tdp1 activity as part of a synergistic treatment for cancer. While this compound has an end-point application in medical research, in plants, its application has not been considered so far. The originality of our study consists in the use of hTdp1 inhibitor in Medicago truncatula cells, which, unlike human cells, contain two Tdp1 genes. Hence, the purpose of this study was to test the hTdp1 inhibitor NSC120686 as an exploratory tool to investigate the plant Tdp1 genes, since their characterization is still in incipient phases. To do so, M. truncatula calli were exposed to increasing (75, 150, 300 μM) concentrations of NSC120686. The levels of cell mortality and DNA damage, measured via diffusion assay and comet assay, respectively, were significantly increased when the highest doses were used, indicative of a cytotoxic and genotoxic threshold. In addition, the NSC120686-treated calli and untreated MtTdp1α-depleted calli shared a similar response in terms of programmed cell death (PCD)/necrosis and DNA damage. Interestingly, the expression profiles of MtTdp1α and MtTdp1β genes were differently affected by the NSC120686 treatment, as MtTdp1α was upregulated while MtTdp1β was downregulated. The NSC120686 treatment affected not only the MtTdp1 genes but also other genes with roles in alternative DNA repair pathways. Since the expression patterns of these genes were different than what was observed in the MtTdp1α-depleted plants, it could be hypothesized that the NSC120686 treatment exerts a different influence compared to that resulting from the lack of the MtTdp1α gene function.
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Affiliation(s)
- Anca Macovei
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100 Pavia, Italy.
| | - Andrea Pagano
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100 Pavia, Italy.
| | - Maria Elisa Sabatini
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100 Pavia, Italy.
| | - Sofia Grandi
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100 Pavia, Italy.
| | - Alma Balestrazzi
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100 Pavia, Italy.
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9
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Huang HC, Liu J, Baglo Y, Rizvi I, Anbil S, Pigula M, Hasan T. Mechanism-informed Repurposing of Minocycline Overcomes Resistance to Topoisomerase Inhibition for Peritoneal Carcinomatosis. Mol Cancer Ther 2018; 17:508-520. [PMID: 29167313 PMCID: PMC5805648 DOI: 10.1158/1535-7163.mct-17-0568] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 09/11/2017] [Accepted: 11/16/2017] [Indexed: 01/04/2023]
Abstract
Mechanism-inspired drug repurposing that augments standard treatments offers a cost-effective and rapid route toward addressing the burgeoning problem of plateauing of effective therapeutics for drug-resistant micrometastases. We show that the antibiotic minocycline, by its ability to minimize DNA repair via reduced expression of tyrosyl-DNA phosphodiesterase-1 (Tdp1), removes a key process attenuating the efficacy of irinotecan, a frequently used chemotherapeutic against metastatic disease. Moreover, minocycline and irinotecan cooperatively mitigate each other's undesired cytokine inductions of VEGF and IL8, respectively, thereby reinforcing the benefits of each modality. These mechanistic interactions result in synergistic enhancement of irinotecan-induced platinum-resistant epithelial ovarian cancer cell death, reduced micrometastases in the omenta and mesentery by >75%, and an extended overall survival by 50% in a late-stage peritoneal carcinomatosis mouse model. Economic incentives and easy translatability make the repurposing of minocycline as a reinforcer of the topoisomerase class of chemotherapeutics extremely valuable and merits further investigations. Mol Cancer Ther; 17(2); 508-20. ©2017 AACR.
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Affiliation(s)
- Huang-Chiao Huang
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts
| | - Joyce Liu
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts
| | - Yan Baglo
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts
- Department of Cancer Research and Molecular Medicine, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Imran Rizvi
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts
| | - Sriram Anbil
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts
- The University of Texas School of Medicine at San Antonio, San Antonio, Texas
| | - Michael Pigula
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts
| | - Tayyaba Hasan
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts
- Division of Health Sciences and Technology, Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts
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10
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Tian LW, Feng Y, Tran TD, Shimizu Y, Pfeifer T, Vu HT, Quinn RJ. Achyrodimer F, a tyrosyl-DNA phosphodiesterase I inhibitor from an Australian fungus of the family Cortinariaceae. Bioorg Med Chem Lett 2017; 27:4007-4010. [PMID: 28797798 DOI: 10.1016/j.bmcl.2017.07.062] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/15/2017] [Accepted: 07/24/2017] [Indexed: 11/24/2022]
Abstract
Mass-guided isolation of the dichloromethane/methanol extracts from a specimen of teleomorphic fungus of the family Cortinariaceae resulted in the identification of a new dimeric cyclobutane metabolite, achyrodimer F (1), along with the monomers hispidin (2) and bisnoryangonin (3). Their structures were determined by NMR and MS data analyses. Density Function Theory (DFT) NMR calculations was employed to confirm the chemical structure of achyrodimer F. Compound 1 inhibited tyrosyl-DNA phosphodiesterase I with an IC50 value of 1μM.
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Affiliation(s)
- Li-Wen Tian
- Griffith Institute for Drug Discovery, Griffith University, Brisbane QLD 4111, Australia
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, Brisbane QLD 4111, Australia
| | - Trong D Tran
- Griffith Institute for Drug Discovery, Griffith University, Brisbane QLD 4111, Australia
| | - Yoko Shimizu
- Centre for Drug Research and Development, Vancouver, British Columbia V6T1Z3, Canada
| | - Tom Pfeifer
- Centre for Drug Research and Development, Vancouver, British Columbia V6T1Z3, Canada
| | - Hoan T Vu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane QLD 4111, Australia
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane QLD 4111, Australia.
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11
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Gushchina I, Nilov D, Zakharenko A, Lavrik O, Švedas V. Structure Modeling of Human Tyrosyl-DNA Phosphodiesterase 1 and Screening for Its Inhibitors. Acta Naturae 2017; 9:59-66. [PMID: 28740727 PMCID: PMC5509001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 11/15/2022] Open
Abstract
The DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (Tdp1) represents a potential molecular target for anticancer therapy. A human Tdp1 model has been constructed using the methods of quantum and molecular mechanics, taking into account the ionization states of the amino acid residues in the active site and their interactions with the substrate and competitive inhibitors. The oligonucleotide- and phosphotyrosine-binding cavities important for the inhibitor design have been identified in the enzyme's active site. The developed molecular model allowed us to uncover new Tdp1 inhibitors whose sulfo group is capable of occupying the position of the 3'-phosphate group of the substrate and forming hydrogen bonds with Lys265, Lys495, and other amino acid residues in the phosphotyrosine binding site.
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Affiliation(s)
- I.V. Gushchina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Lenin Hills 1, bldg. 73, Moscow, 119991, Russia
| | - D.K. Nilov
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Lenin Hills 1 , bldg. 40, Moscow, 119991, Russia
| | - A.L. Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Lavrentiev avenue 8, Novosibirsk, 630090, Russia
| | - O.I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Lavrentiev avenue 8, Novosibirsk, 630090, Russia
- Altai State University, Lenin avenue 61, Barnaul, 656049, Russia
| | - V.K. Švedas
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Lenin Hills 1, bldg. 73, Moscow, 119991, Russia
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Lenin Hills 1 , bldg. 40, Moscow, 119991, Russia
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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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13
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Depletion of tyrosyl DNA phosphodiesterase 2 activity enhances etoposide-mediated double-strand break formation and cell killing. DNA Repair (Amst) 2016; 43:38-47. [DOI: 10.1016/j.dnarep.2016.04.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 11/20/2022]
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14
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Nikolic K, Mavridis L, Djikic T, Vucicevic J, Agbaba D, Yelekci K, Mitchell JBO. Drug Design for CNS Diseases: Polypharmacological Profiling of Compounds Using Cheminformatic, 3D-QSAR and Virtual Screening Methodologies. Front Neurosci 2016; 10:265. [PMID: 27375423 PMCID: PMC4901078 DOI: 10.3389/fnins.2016.00265] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/25/2016] [Indexed: 11/13/2022] Open
Abstract
HIGHLIGHTSMany CNS targets are being explored for multi-target drug design New databases and cheminformatic methods enable prediction of primary pharmaceutical target and off-targets of compounds QSAR, virtual screening and docking methods increase the potential of rational drug design
The diverse cerebral mechanisms implicated in Central Nervous System (CNS) diseases together with the heterogeneous and overlapping nature of phenotypes indicated that multitarget strategies may be appropriate for the improved treatment of complex brain diseases. Understanding how the neurotransmitter systems interact is also important in optimizing therapeutic strategies. Pharmacological intervention on one target will often influence another one, such as the well-established serotonin-dopamine interaction or the dopamine-glutamate interaction. It is now accepted that drug action can involve plural targets and that polypharmacological interaction with multiple targets, to address disease in more subtle and effective ways, is a key concept for development of novel drug candidates against complex CNS diseases. A multi-target therapeutic strategy for Alzheimer‘s disease resulted in the development of very effective Multi-Target Designed Ligands (MTDL) that act on both the cholinergic and monoaminergic systems, and also retard the progression of neurodegeneration by inhibiting amyloid aggregation. Many compounds already in databases have been investigated as ligands for multiple targets in drug-discovery programs. A probabilistic method, the Parzen-Rosenblatt Window approach, was used to build a “predictor” model using data collected from the ChEMBL database. The model can be used to predict both the primary pharmaceutical target and off-targets of a compound based on its structure. Several multi-target ligands were selected for further study, as compounds with possible additional beneficial pharmacological activities. Based on all these findings, it is concluded that multipotent ligands targeting AChE/MAO-A/MAO-B and also D1-R/D2-R/5-HT2A-R/H3-R are promising novel drug candidates with improved efficacy and beneficial neuroleptic and procognitive activities in treatment of Alzheimer's and related neurodegenerative diseases. Structural information for drug targets permits docking and virtual screening and exploration of the molecular determinants of binding, hence facilitating the design of multi-targeted drugs. The crystal structures and models of enzymes of the monoaminergic and cholinergic systems have been used to investigate the structural origins of target selectivity and to identify molecular determinants, in order to design MTDLs.
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Affiliation(s)
- Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade Belgrade, Serbia
| | - Lazaros Mavridis
- School of Biological and Chemical Sciences, Queen Mary University of London London, UK
| | - Teodora Djikic
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University Istanbul, Turkey
| | - Jelica Vucicevic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade Belgrade, Serbia
| | - Danica Agbaba
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade Belgrade, Serbia
| | - Kemal Yelekci
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University Istanbul, Turkey
| | - John B O Mitchell
- EaStCHEM School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews St Andrews, UK
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15
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Ahmadi M, Nowroozi A, Shahlaei M. Constructing an atomic-resolution model of human P2X7 receptor followed by pharmacophore modeling to identify potential inhibitors. J Mol Graph Model 2015; 61:243-61. [PMID: 26298810 DOI: 10.1016/j.jmgm.2015.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 06/22/2015] [Accepted: 08/10/2015] [Indexed: 12/22/2022]
Abstract
The P2X purinoceptor 7 (P2X7R) is a trimeric ATP-activated ion channel gated by extracellular ATP. P2X7R has important role in numerous diseases including pain, neurodegeneration, and inflammatory diseases such as rheumatoid arthritis and osteoarthritis. In this prospective, the discovery of small-molecule inhibitors for P2X7R as a novel therapeutic target has received considerable attention in recent years. At first, 3D structure of P2X7R was built by using homology modeling (HM) and a 50ns molecular dynamics simulation (MDS). Ligand-based quantitative pharmacophore modeling methodology of P2X7R antagonists were developed based on training set of 49 compounds. The best four-feature pharmacophore model, includes two hydrophobic aromatic, one hydrophobic and one aromatic ring features, has the highest correlation coefficient (0.874), cost difference (368.677), low RMSD (2.876), as well as it shows a high goodness of fit and enrichment factor. Consequently, some hit compounds were introduced as final candidates by employing virtual screening and molecular docking procedure simultaneously. Among these compounds, six potential molecule were identified as potential virtual leads which, as such or upon further optimization, can be used to design novel P2X7R inhibitors.
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Affiliation(s)
- Mehdi Ahmadi
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amin Nowroozi
- Pharmaceutical sciences Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Shahlaei
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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16
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Nguyen TX, Abdelmalak M, Marchand C, Agama K, Pommier Y, Cushman M. Synthesis and biological evaluation of nitrated 7-, 8-, 9-, and 10-hydroxyindenoisoquinolines as potential dual topoisomerase I (Top1)-tyrosyl-DNA phosphodiesterase I (TDP1) inhibitors. J Med Chem 2015; 58:3188-208. [PMID: 25811317 PMCID: PMC7747014 DOI: 10.1021/acs.jmedchem.5b00136] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The structure-activity relationships and hit-to-lead optimization of dual Top1-TDP1 inhibitors in the indenoisoquinoline drug class were investigated. A series of nitrated 7-, 8-, 9-, and 10-hydroxyindenoisoquinolines were synthesized and evaluated. Several compounds displayed potent dual Top1-TDP1 inhibition. The 9-hydroxy series exhibited potencies and cytotoxicities vs Top1 that surpassed those of camptothecin (CPT), the natural alkaloid that is being used as a standard in the Top1-mediated DNA cleavage assay. One member of this series was a more potent Top1 inhibitor at a concentration of 5 nM and produced a more stable ternary drug-DNA-Top1 cleavage complex than CPT.
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Affiliation(s)
- Trung Xuan Nguyen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Monica Abdelmalak
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892-4255, United States
| | - Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892-4255, United States
| | - Keli Agama
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892-4255, United States
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892-4255, United States
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
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17
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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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18
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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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19
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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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20
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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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Drwal MN, Griffith R. Combination of ligand- and structure-based methods in virtual screening. DRUG DISCOVERY TODAY. TECHNOLOGIES 2013; 10:e395-e401. [PMID: 24050136 DOI: 10.1016/j.ddtec.2013.02.002] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The combination of ligand- and structure-based molecular modelling methods has become a common approach in virtual screening. This review describes different strategies for integration of ligand- and structure-based methods which can be divided into sequential, parallel or hybrid approaches. Although no thorough performance comparisons between combined approaches are available, examples of successful applications in prospective and retrospective virtual screening are discussed. Most published studies use a sequential approach, utilising well-documented single methods successfully.
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Takagi M, Ueda JY, Hwang JH, Hashimoto J, Izumikawa M, Murakami H, Sekido Y, Shin-ya K. Tyrosyl-DNA phosphodiesterase 1 inhibitor from an anamorphic fungus. JOURNAL OF NATURAL PRODUCTS 2012; 75:764-767. [PMID: 22390627 DOI: 10.1021/np2007389] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is an enzyme that catalyzes hydrolysis of 3'-phosphotyrosyl bonds and is involved in repair of irreversible topoisomerase I (Top1)-DNA covalent complexes. Tdp1 inhibitors are regarded as potential cancer therapeutics in combination with Top1 inhibitors, which are currently used to treat human cancers. While screening for Tdp1 inhibitors, we discovered a novel compound, JBIR-21 (1), from the culture of an anamorphic fungus, RF-13305. The structure of 1 was established by extensive NMR and MS analyses. Compound 1 showed inhibitory activity against Tdp1 (IC(50) value, 18 μM) and cytotoxic activity against cancer cell lines (IC(50) values, 3.5-13 μM). Compound 1 also exhibited antitumor activity in a mouse xenograft model without adverse effects.
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Affiliation(s)
- Motoki Takagi
- Biomedicinal Information Research Center (BIRC), Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Tokyo 135-0064, Japan.
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Perego P, Cossa G, Tinelli S, Corna E, Carenini N, Gatti L, De Cesare M, Ciusani E, Zunino F, Luison E, Canevari S, Zaffaroni N, Beretta GL. Role of tyrosyl-DNA phosphodiesterase 1 and inter-players in regulation of tumor cell sensitivity to topoisomerase I inhibition. Biochem Pharmacol 2012; 83:27-36. [DOI: 10.1016/j.bcp.2011.09.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 09/15/2011] [Accepted: 09/19/2011] [Indexed: 11/30/2022]
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