1
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Nao SC, Huang LS, Shiu-Hin Chan D, Wang X, Li GD, Wu J, Wong CY, Wang W, Leung CH. Repurposing sodium stibogluconate as an uracil DNA glycosylase inhibitor against prostate cancer using a time-resolved oligonucleotide-based drug screening platform. Bioorg Chem 2024; 144:107176. [PMID: 38330721 DOI: 10.1016/j.bioorg.2024.107176] [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] [Received: 11/10/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
Repurposing drugs can significantly reduce the time and costs associated with drug discovery and development. However, many drug compounds possess intrinsic fluorescence, resulting in aberrations such as auto-fluorescence, scattering and quenching, in fluorescent high-throughput screening assays. To overcome these drawbacks, time-resolved technologies have received increasing attention. In this study, we have developed a rapid and efficient screening platform based on time-resolved emission spectroscopy in order to screen for inhibitors of the DNA repair enzyme, uracil-DNA glycosylase (UDG). From a database of 1456 FDA/EMA-approved drugs, sodium stibogluconate was discovered as a potent UDG inhibitor. This compound showed synergistic cytotoxicity against 5-fluorouracil-resistant cancer cells. This work provides a promising future for time-resolved technologies for high-throughput screening (HTS), allowing for the swift identification of bioactive compounds from previously overlooked scaffolds due to their inherent fluorescence properties.
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Affiliation(s)
- Sang-Cuo Nao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
| | - Le-Sheng Huang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
| | | | - Xueliang Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China
| | - Guo-Dong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
| | - Jia Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
| | - Chun-Yuen Wong
- Department of Chemistry, City University of Hong Kong, Hong Kong, China.
| | - Wanhe Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China.
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China; Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Macao Centre for Research and Development in Chinese Medicine, University of Macau, Taipa, Macau, China; MoE Frontiers Science Centre for Precision Oncology, University of Macau, Taipa, Macau, China.
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2
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Raj P, Selvam K, Roy K, Mani Tripathi S, Kesharwani S, Gopal B, Varshney U, Sundriyal S. Identification of a new and diverse set of Mycobacterium tuberculosstais uracil-DNA glycosylase (MtUng) inhibitors using structure-based virtual screening: experimental validation and molecular dynamics studies. Bioorg Med Chem Lett 2022; 76:129008. [PMID: 36174837 DOI: 10.1016/j.bmcl.2022.129008] [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] [Received: 07/28/2022] [Revised: 09/18/2022] [Accepted: 09/23/2022] [Indexed: 11/19/2022]
Abstract
Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng), a key DNA repair enzyme, represents an attractive target for the design of new antimycobacterial agents. However, only a limited number of weak MtUng inhibitors are reported, primarily based on the uracil ring, and hence, lack diversity. We report the first structure-based virtual screening (SBVS) using three separate libraries consisting of uracil and non-uracil small molecules, together with the FDA-approved drugs. Twenty diverse virtual hits with the highest predicted binding were procured and screened using a fluorescence-based assay to evaluate their potential to inhibit MtUng. Several of these molecules were found to inhibit MtUng activity at low mM and µM levels, comparable to or better than several other reported Ung inhibitors. Thus, these molecules represent a diverse set of scaffolds for developing next-generation MtUng inhibitors. The most active uracil-based compound 5 (IC50 = 0.14 mM) was found to be ∼15-fold more potent than the positive control, uracil. The binding stability and conformation of compound 5 in complex with the enzyme were further confirmed using molecular dynamics simulation.
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Affiliation(s)
- Prateek Raj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Karthik Selvam
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Koyel Roy
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Shailesh Mani Tripathi
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India
| | - Sharyu Kesharwani
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India
| | | | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Sandeep Sundriyal
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan 333031, India.
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3
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A New Class of Uracil-DNA Glycosylase Inhibitors Active against Human and Vaccinia Virus Enzyme. Molecules 2021; 26:molecules26216668. [PMID: 34771075 PMCID: PMC8587785 DOI: 10.3390/molecules26216668] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/24/2021] [Accepted: 10/30/2021] [Indexed: 11/17/2022] Open
Abstract
Uracil-DNA glycosylases are enzymes that excise uracil bases appearing in DNA as a result of cytosine deamination or accidental dUMP incorporation from the dUTP pool. The activity of Family 1 uracil-DNA glycosylase (UNG) activity limits the efficiency of antimetabolite drugs and is essential for virulence in some bacterial and viral infections. Thus, UNG is regarded as a promising target for antitumor, antiviral, antibacterial, and antiprotozoal drugs. Most UNG inhibitors presently developed are based on the uracil base linked to various substituents, yet new pharmacophores are wanted to target a wide range of UNGs. We have conducted virtual screening of a 1,027,767-ligand library and biochemically screened the best hits for the inhibitory activity against human and vaccinia virus UNG enzymes. Although even the best inhibitors had IC50 ≥ 100 μM, they were highly enriched in a common fragment, tetrahydro-2,4,6-trioxopyrimidinylidene (PyO3). In silico, PyO3 preferably docked into the enzyme's active site, and in kinetic experiments, the inhibition was better consistent with the competitive mechanism. The toxicity of two best inhibitors for human cells was independent of the presence of methotrexate, which is consistent with the hypothesis that dUMP in genomic DNA is less toxic for the cell than strand breaks arising from the massive removal of uracil. We conclude that PyO3 may be a novel pharmacophore with the potential for development into UNG-targeting agents.
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4
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5
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Viruses with U-DNA: New Avenues for Biotechnology. Viruses 2021; 13:v13050875. [PMID: 34068736 PMCID: PMC8150378 DOI: 10.3390/v13050875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023] Open
Abstract
Deoxyuridine in DNA has recently been in the focus of research due to its intriguing roles in several physiological and pathophysiological situations. Although not an orthodox DNA base, uracil may appear in DNA via either cytosine deamination or thymine-replacing incorporations. Since these alterations may induce mutation or may perturb DNA–protein interactions, free living organisms from bacteria to human contain several pathways to counteract uracilation. These efficient and highly specific repair routes uracil-directed excision repair initiated by representative of uracil-DNA glycosylase families. Interestingly, some bacteriophages exist with thymine-lacking uracil-DNA genome. A detailed understanding of the strategy by which such phages can replicate in bacteria where an efficient repair pathway functions for uracil-excision from DNA is expected to reveal novel inhibitors that can also be used for biotechnological applications. Here, we also review the several potential biotechnological applications already implemented based on inhibitors of uracil-excision repair, such as Crispr-base-editing and detection of nascent uracil distribution pattern in complex genomes.
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6
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Nguyen MT, Moiani D, Ahmed Z, Arvai AS, Namjoshi S, Shin DS, Fedorov Y, Selvik EJ, Jones DE, Pink J, Yan Y, Laverty DJ, Nagel ZD, Tainer JA, Gerson SL. An effective human uracil-DNA glycosylase inhibitor targets the open pre-catalytic active site conformation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:143-159. [PMID: 33675849 PMCID: PMC8722130 DOI: 10.1016/j.pbiomolbio.2021.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/13/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Human uracil DNA-glycosylase (UDG) is the prototypic and first identified DNA glycosylase with a vital role in removing deaminated cytosine and incorporated uracil and 5-fluorouracil (5-FU) from DNA. UDG depletion sensitizes cells to high APOBEC3B deaminase and to pemetrexed (PEM) and floxuridine (5-FdU), which are toxic to tumor cells through incorporation of uracil and 5-FU into DNA. To identify small-molecule UDG inhibitors for pre-clinical evaluation, we optimized biochemical screening of a selected diversity collection of >3,000 small-molecules. We found aurintricarboxylic acid (ATA) as an inhibitor of purified UDG at an initial calculated IC50 < 100 nM. Subsequent enzymatic assays confirmed effective ATA inhibition but with an IC50 of 700 nM and showed direct binding to the human UDG with a KD of <700 nM. ATA displays preferential, dose-dependent binding to purified human UDG compared to human 8-oxoguanine DNA glycosylase. ATA did not bind uracil-containing DNA at these concentrations. Yet, combined crystal structure and in silico docking results unveil ATA interactions with the DNA binding channel and uracil-binding pocket in an open, destabilized UDG conformation. Biologically relevant ATA inhibition of UDG was measured in cell lysates from human DLD1 colon cancer cells and in MCF-7 breast cancer cells using a host cell reactivation assay. Collective findings provide proof-of-principle for development of an ATA-based chemotype and “door stopper” strategy targeting inhibitor binding to a destabilized, open pre-catalytic glycosylase conformation that prevents active site closing for functional DNA binding and nucleotide flipping needed to excise altered bases in DNA.
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Affiliation(s)
- My T Nguyen
- Case Western Reserve University, Department of Biochemistry, Cleveland, OH, 44106, USA
| | - Davide Moiani
- Departments of Cancer Biology and of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcomb Blvd, Houston, TX, 77030, USA
| | - Zamal Ahmed
- Departments of Cancer Biology and of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcomb Blvd, Houston, TX, 77030, USA
| | - Andrew S Arvai
- Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Sarita Namjoshi
- Departments of Cancer Biology and of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcomb Blvd, Houston, TX, 77030, USA
| | - Dave S Shin
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuriy Fedorov
- Case Small-Molecule Screening Core, School of Medicine, Case Western Reserve University, Cleveland, OH, 44016, USA
| | - Edward J Selvik
- Department of Pharmaceutical Sciences, The University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, AR, 72205, USA
| | - Darin E Jones
- Department of Pharmaceutical Sciences, The University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, AR, 72205, USA
| | - John Pink
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Yan Yan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Daniel J Laverty
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA
| | - Zachary D Nagel
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA
| | - John A Tainer
- Departments of Cancer Biology and of Molecular & Cellular Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcomb Blvd, Houston, TX, 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Stanton L Gerson
- Case Western Reserve University, Department of Biochemistry, Cleveland, OH, 44106, USA; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
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7
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Hans F, Senarisoy M, Bhaskar Naidu C, Timmins J. Focus on DNA Glycosylases-A Set of Tightly Regulated Enzymes with a High Potential as Anticancer Drug Targets. Int J Mol Sci 2020; 21:ijms21239226. [PMID: 33287345 PMCID: PMC7730500 DOI: 10.3390/ijms21239226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 12/01/2020] [Indexed: 12/25/2022] Open
Abstract
Cancer is the second leading cause of death with tens of millions of people diagnosed with cancer every year around the world. Most radio- and chemotherapies aim to eliminate cancer cells, notably by causing severe damage to the DNA. However, efficient repair of such damage represents a common mechanism of resistance to initially effective cytotoxic agents. Thus, development of new generation anticancer drugs that target DNA repair pathways, and more particularly the base excision repair (BER) pathway that is responsible for removal of damaged bases, is of growing interest. The BER pathway is initiated by a set of enzymes known as DNA glycosylases. Unlike several downstream BER enzymes, DNA glycosylases have so far received little attention and the development of specific inhibitors of these enzymes has been lagging. Yet, dysregulation of DNA glycosylases is also known to play a central role in numerous cancers and at different stages of the disease, and thus inhibiting DNA glycosylases is now considered a valid strategy to eliminate cancer cells. This review provides a detailed overview of the activities of DNA glycosylases in normal and cancer cells, their modes of regulation, and their potential as anticancer drug targets.
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8
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Mechetin GV, Endutkin AV, Diatlova EA, Zharkov DO. Inhibitors of DNA Glycosylases as Prospective Drugs. Int J Mol Sci 2020; 21:ijms21093118. [PMID: 32354123 PMCID: PMC7247160 DOI: 10.3390/ijms21093118] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 12/22/2022] Open
Abstract
DNA glycosylases are enzymes that initiate the base excision repair pathway, a major biochemical process that protects the genomes of all living organisms from intrinsically and environmentally inflicted damage. Recently, base excision repair inhibition proved to be a viable strategy for the therapy of tumors that have lost alternative repair pathways, such as BRCA-deficient cancers sensitive to poly(ADP-ribose)polymerase inhibition. However, drugs targeting DNA glycosylases are still in development and so far have not advanced to clinical trials. In this review, we cover the attempts to validate DNA glycosylases as suitable targets for inhibition in the pharmacological treatment of cancer, neurodegenerative diseases, chronic inflammation, bacterial and viral infections. We discuss the glycosylase inhibitors described so far and survey the advances in the assays for DNA glycosylase reactions that may be used to screen pharmacological libraries for new active compounds.
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Affiliation(s)
- Grigory V. Mechetin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
| | - Anton V. Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
| | - Evgeniia A. Diatlova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
| | - Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
- Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Correspondence: ; Tel.: +7-383-363-5187
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9
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Savva R. The Essential Co-Option of Uracil-DNA Glycosylases by Herpesviruses Invites Novel Antiviral Design. Microorganisms 2020; 8:microorganisms8030461. [PMID: 32214054 PMCID: PMC7143999 DOI: 10.3390/microorganisms8030461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 01/10/2023] Open
Abstract
Vast evolutionary distances separate the known herpesviruses, adapted to colonise specialised cells in predominantly vertebrate hosts. Nevertheless, the distinct herpesvirus families share recognisably related genomic attributes. The taxonomic Family Herpesviridae includes many important human and animal pathogens. Successful antiviral drugs targeting Herpesviridae are available, but the need for reduced toxicity and improved efficacy in critical healthcare interventions invites novel solutions: immunocompromised patients presenting particular challenges. A conserved enzyme required for viral fitness is Ung, a uracil-DNA glycosylase, which is encoded ubiquitously in Herpesviridae genomes and also host cells. Research investigating Ung in Herpesviridae dynamics has uncovered an unexpected combination of viral co-option of host Ung, along with remarkable Subfamily-specific exaptation of the virus-encoded Ung. These enzymes apparently play essential roles, both in the maintenance of viral latency and during initiation of lytic replication. The ubiquitously conserved Ung active site has previously been explored as a therapeutic target. However, exquisite selectivity and better drug-like characteristics might instead be obtained via targeting structural variations within another motif of catalytic importance in Ung. The motif structure is unique within each Subfamily and essential for viral survival. This unique signature in highly conserved Ung constitutes an attractive exploratory target for the development of novel beneficial therapeutics.
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Affiliation(s)
- Renos Savva
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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10
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Li G, Henry SA, Liu H, Kang TS, Nao SC, Zhao Y, Wu C, Jin J, Zhang JT, Leung CH, Wai Hong Chan P, Ma DL. A robust photoluminescence screening assay identifies uracil-DNA glycosylase inhibitors against prostate cancer. Chem Sci 2020; 11:1750-1760. [PMID: 34123270 PMCID: PMC8148385 DOI: 10.1039/c9sc05623h] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Many cancers have developed resistance to 5-FU, due to removal by the enzyme uracil-DNA glycosylase (UDG), a type of base excision repair enzyme (BER) that can excise uracil and 5-fluorouracil (5-FU) from DNA. However, the development of UDG inhibitor screening methods, especially for the rapid and efficient screening of natural product/natural product-like compounds, is still limited so far. We developed herein a robust time-resolved photoluminescence method for screening UDG inhibitors, which could significantly improve sensitivity over the screening method based on the conventional steady-state spectroscopy, reducing the substantial fluorescence background interference. As a proof-of-concept, two potential UDG inhibitors were identified from a database of natural products and approved drugs. Co-treatment of these two compounds with 5-FU showed synergistic cytotoxicity, providing the basis for treating drug-resistant cancers. Overall, this method provides an avenue for the rapid screening of small molecule regulators of other BER enzyme activities that can avoid false negatives arising from the background fluorescence. The discovery of UDG inhibitors against prostate cancer by using a robust photoluminescence screening assay that can avoid false negatives arising from the background fluorescence.![]()
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Affiliation(s)
- Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau Macau
| | | | - Hao Liu
- Department of Chemistry, Hong Kong Baptist University Kowloon Tong Hong Kong
| | - Tian-Shu Kang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau Macau
| | - Sang-Cuo Nao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau Macau
| | - Yichao Zhao
- School of Chemistry, Monash University Clayton Victoria 3800 Australia
| | - Chun Wu
- Department of Chemistry, Hong Kong Baptist University Kowloon Tong Hong Kong
| | - Jianwen Jin
- School of Chemistry, Monash University Clayton Victoria 3800 Australia
| | - Jia-Tong Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau Macau
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau Macau
| | - Philip Wai Hong Chan
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK.,School of Chemistry, Monash University Clayton Victoria 3800 Australia
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University Kowloon Tong Hong Kong
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11
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Michel M, Visnes T, Homan EJ, Seashore-Ludlow B, Hedenström M, Wiita E, Vallin K, Paulin CBJ, Zhang J, Wallner O, Scobie M, Schmidt A, Jenmalm-Jensen A, Warpman Berglund U, Helleday T. Computational and Experimental Druggability Assessment of Human DNA Glycosylases. ACS OMEGA 2019; 4:11642-11656. [PMID: 31460271 PMCID: PMC6682003 DOI: 10.1021/acsomega.9b00162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/21/2019] [Indexed: 06/10/2023]
Abstract
Due to a polar or even charged binding interface, DNA-binding proteins are considered extraordinarily difficult targets for development of small-molecule ligands and only a handful of proteins have been targeted successfully to date. Recently, however, it has been shown that development of selective and efficient inhibitors of 8-oxoguanine DNA glycosylase is possible. Here, we describe the initial druggability assessment of DNA glycosylases in a computational setting and experimentally investigate several methods to target endonuclease VIII-like 1 (NEIL1) with small-molecule inhibitors. We find that DNA glycosylases exhibit good predicted druggability in both DNA-bound and -unbound states. Furthermore, we find catalytic sites to be highly flexible, allowing for a range of interactions and binding partners. One flexible catalytic site was rationalized for NEIL1 and further investigated experimentally using both a biochemical assay in the presence of DNA and a thermal shift assay in the absence of DNA.
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Affiliation(s)
- Maurice Michel
- Science
for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Torkild Visnes
- Science
for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
- Department
of Biotechnology and Nanomedicine, SINTEF
Industry, N-7465 Trondheim, Norway
| | - Evert J. Homan
- Science
for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Brinton Seashore-Ludlow
- Chemical
Biology Consortium Sweden, Science for Life Laboratory, Division of
Translational Medicine and Chemical Biology, Department of Medical
Biochemistry and Biophysics, Karolinska
Institutet, S-171 21 Stockholm, Sweden
| | | | - Elisée Wiita
- Science
for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Karl Vallin
- Science
for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Cynthia B. J. Paulin
- Science
for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Jiaxi Zhang
- Institute
of Organic Chemistry, Clausthal University
of Technology, Leibnizstrasse
6, D-38678 Clausthal-Zellerfeld, Germany
| | - Olov Wallner
- Science
for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Martin Scobie
- Science
for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Andreas Schmidt
- Institute
of Organic Chemistry, Clausthal University
of Technology, Leibnizstrasse
6, D-38678 Clausthal-Zellerfeld, Germany
| | - Annika Jenmalm-Jensen
- Chemical
Biology Consortium Sweden, Science for Life Laboratory, Division of
Translational Medicine and Chemical Biology, Department of Medical
Biochemistry and Biophysics, Karolinska
Institutet, S-171 21 Stockholm, Sweden
| | - Ulrika Warpman Berglund
- Science
for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Thomas Helleday
- Science
for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
- Sheffield
Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, S10 2RX Sheffield, U.K.
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12
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Targeting uracil-DNA glycosylases for therapeutic outcomes using insights from virus evolution. Future Med Chem 2019; 11:1323-1344. [PMID: 31161802 DOI: 10.4155/fmc-2018-0319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Ung-type uracil-DNA glycosylases are frontline defenders of DNA sequence fidelity in bacteria, plants and animals; Ungs also directly assist both innate and humoral immunity. Critically important in viral pathogenesis, whether acting for or against viral DNA persistence, Ungs also have therapeutic relevance to cancer, microbial and parasitic diseases. Ung catalytic specificity is uniquely conserved, yet selective antiviral drugging of the Ung catalytic pocket is tractable. However, more promising precision therapy approaches present themselves via insights from viral strategies, including sequestration or adaptation of Ung for noncanonical roles. A universal Ung inhibition mechanism, converged upon by unrelated viruses, could also inform design of compounds to inhibit specific distinct Ungs. Extrapolating current developments, the character of such novel chemical entities is proposed.
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13
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Visnes T, Grube M, Hanna BMF, Benitez-Buelga C, Cázares-Körner A, Helleday T. Targeting BER enzymes in cancer therapy. DNA Repair (Amst) 2018; 71:118-126. [PMID: 30228084 DOI: 10.1016/j.dnarep.2018.08.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Base excision repair (BER) repairs mutagenic or genotoxic DNA base lesions, thought to be important for both the etiology and treatment of cancer. Cancer phenotypic stress induces oxidative lesions, and deamination products are responsible for one of the most prevalent mutational signatures in cancer. Chemotherapeutic agents induce genotoxic DNA base damage that are substrates for BER, while synthetic lethal approaches targeting BER-related factors are making their way into the clinic. Thus, there are three strategies by which BER is envisioned to be relevant in cancer chemotherapy: (i) to maintain cellular growth in the presence of endogenous DNA damage in stressed cancer cells, (ii) to maintain viability after exogenous DNA damage is introduced by therapeutic intervention, or (iii) to confer synthetic lethality in cancer cells that have lost one or more additional DNA repair pathways. Here, we discuss the potential treatment strategies, and briefly summarize the progress that has been made in developing inhibitors to core BER-proteins and related factors.
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Affiliation(s)
- Torkild Visnes
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden; Department of Biotechnology and Nanomedicine, SINTEF Industry, N-7034 Trondheim, Norway
| | - Maurice Grube
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Bishoy Magdy Fekry Hanna
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Carlos Benitez-Buelga
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Armando Cázares-Körner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden; Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK.
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14
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Arif SM, Geethanandan K, Mishra P, Surolia A, Varshney U, Vijayan M. Structural plasticity inMycobacterium tuberculosisuracil-DNA glycosylase (MtUng) and its functional implications. ACTA ACUST UNITED AC 2015; 71:1514-27. [DOI: 10.1107/s1399004715009311] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/15/2015] [Indexed: 12/29/2022]
Abstract
17 independent crystal structures of family I uracil-DNA glycosylase fromMycobacterium tuberculosis(MtUng) and its complexes with uracil and its derivatives, distributed among five distinct crystal forms, have been determined. Thermodynamic parameters of binding in the complexes have been measured using isothermal titration calorimetry. The two-domain protein exhibits open and closed conformations, suggesting that the closure of the domain on DNA binding involves conformational selection. Segmental mobility in the enzyme molecule is confined to a 32-residue stretch which plays a major role in DNA binding. Uracil and its derivatives can bind to the protein in two possible orientations. Only one of them is possible when there is a bulky substituent at the 5′ position. The crystal structures of the complexes provide a reasonable rationale for the observed thermodynamic parameters. In addition to providing fresh insights into the structure, plasticity and interactions of the protein molecule, the results of the present investigation provide a platform for structure-based inhibitor design.
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15
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Biela A, Coste F, Culard F, Guerin M, Goffinont S, Gasteiger K, Cieśla J, Winczura A, Kazimierczuk Z, Gasparutto D, Carell T, Tudek B, Castaing B. Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization. Nucleic Acids Res 2014; 42:10748-61. [PMID: 25143530 PMCID: PMC4176347 DOI: 10.1093/nar/gku613] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
DNA glycosylases from the Fpg/Nei structural superfamily are base excision repair enzymes involved in the removal of a wide variety of mutagen and potentially lethal oxidized purines and pyrimidines. Although involved in genome stability, the recent discovery of synthetic lethal relationships between DNA glycosylases and other pathways highlights the potential of DNA glycosylase inhibitors for future medicinal chemistry development in cancer therapy. By combining biochemical and structural approaches, the physical target of 2-thioxanthine (2TX), an uncompetitive inhibitor of Fpg, was identified. 2TX interacts with the zinc finger (ZnF) DNA binding domain of the enzyme. This explains why the zincless hNEIL1 enzyme is resistant to 2TX. Crystal structures of the enzyme bound to DNA in the presence of 2TX demonstrate that the inhibitor chemically reacts with cysteine thiolates of ZnF and induces the loss of zinc. The molecular mechanism by which 2TX inhibits Fpg may be generalized to all prokaryote and eukaryote ZnF-containing Fpg/Nei-DNA glycosylases. Cell experiments show that 2TX can operate in cellulo on the human Fpg/Nei DNA glycosylases. The atomic elucidation of the determinants for the interaction of 2TX to Fpg provides the foundation for the future design and synthesis of new inhibitors with high efficiency and selectivity.
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Affiliation(s)
- Artur Biela
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45100 Orléans cedex02, France Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Franck Coste
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45100 Orléans cedex02, France
| | - Françoise Culard
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45100 Orléans cedex02, France
| | - Martine Guerin
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45100 Orléans cedex02, France
| | - Stéphane Goffinont
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45100 Orléans cedex02, France
| | - Karola Gasteiger
- Department of Chemistry, Ludwig-Maximilians-Universität (LMU), Butenandtstr. 5-13 (Haus F), München D-81377, Germany
| | - Jarosław Cieśla
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Alicja Winczura
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Zygmunt Kazimierczuk
- Institute of Chemistry, Warsaw University of Life Sciences, 159C Nowoursynowska St., 02-787 Warsaw, Poland
| | - Didier Gasparutto
- Laboratoire Lésions des Acides Nucléiques, SCIB/UMR E3 CEA-UJF, INAC, CEA, Grenoble, France
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-Universität (LMU), Butenandtstr. 5-13 (Haus F), München D-81377, Germany
| | - Barbara Tudek
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland Institute of Genetics and Biotechnology, Warsaw University, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45100 Orléans cedex02, France
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16
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Ulrich S, Dumy P. Probing secondary interactions in biomolecular recognition by dynamic combinatorial chemistry. Chem Commun (Camb) 2014; 50:5810-25. [DOI: 10.1039/c4cc00263f] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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17
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Inhibition of DNA glycosylases via small molecule purine analogs. PLoS One 2013; 8:e81667. [PMID: 24349107 PMCID: PMC3857224 DOI: 10.1371/journal.pone.0081667] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 10/16/2013] [Indexed: 11/19/2022] Open
Abstract
Following the formation of oxidatively-induced DNA damage, several DNA glycosylases are required to initiate repair of the base lesions that are formed. Recently, NEIL1 and other DNA glycosylases, including OGG1 and NTH1 were identified as potential targets in combination chemotherapeutic strategies. The potential therapeutic benefit for the inhibition of DNA glycosylases was validated by demonstrating synthetic lethality with drugs that are commonly used to limit DNA replication through dNTP pool depletion via inhibition of thymidylate synthetase and dihydrofolate reductase. Additionally, NEIL1-associated synthetic lethality has been achieved in combination with Fanconi anemia, group G. As a prelude to the development of strategies to exploit the potential benefits of DNA glycosylase inhibition, it was necessary to develop a reliable high-throughput screening protocol for this class of enzymes. Using NEIL1 as the proof-of-principle glycosylase, a fluorescence-based assay was developed that utilizes incision of site-specifically modified oligodeoxynucleotides to detect enzymatic activity. This assay was miniaturized to a 1536-well format and used to screen small molecule libraries for inhibitors of the combined glycosylase/AP lyase activities. Among the top hits of these screens were several purine analogs, whose postulated presence in the active site of NEIL1 was consistent with the paradigm of NEIL1 recognition and excision of damaged purines. Although a subset of these small molecules could inhibit other DNA glycosylases that excise oxidatively-induced DNA adducts, they could not inhibit a pyrimidine dimer-specific glycosylase.
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18
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Eldin P, Chazal N, Fenard D, Bernard E, Guichou JF, Briant L. Vpr expression abolishes the capacity of HIV-1 infected cells to repair uracilated DNA. Nucleic Acids Res 2013; 42:1698-710. [PMID: 24178031 PMCID: PMC3919559 DOI: 10.1093/nar/gkt974] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) Vpr protein binds to the cellular uracil–DNA glycosylase UNG2 and induces its degradation through the assembly with the DDB1-CUL4 ubiquitin ligase complex. This interaction counteracts the antiviral activity exerted by UNG2 on HIV-1 gene transcription, as previously reported by us. In this work, we show that Vpr expression in the context of HIV-1 infection markedly decreases UNG2 expression in transformed or primary CD4+ T lymphocytes. We demonstrate for the first time that Vpr-UNG2 interaction significantly impairs the uracil excision activity of infected cells. The loss of uracil excision activity coincides with a significant accumulation of uracilated bases in the genome of infected cells without changes in cell division. Although UNG2 expression and uracil–DNA glycosylase activity are recovered after the peak of retroviral replication, the mutagenic effect of transient DNA uracilation in cycling cells should be taken into account. Therefore, the possible consequences of Vpr-mediated temporary depletion of endogenous nuclear UNG2 and subsequent alteration of the genomic integrity of infected cells need to be evaluated in the physiopathogenesis of HIV infection.
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Affiliation(s)
- Patrick Eldin
- Centre d'étude d'agents Pathogènes et Biotechnologies pour la Santé (CPBS) - UMR 5236-CNRS - Université Montpellier 1 and 2, Montpellier, France and Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, Université Montpellier 1 and 2, Montpellier, France
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19
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Svedružić ŽM. Dnmt1 structure and function. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:221-54. [PMID: 21507353 DOI: 10.1016/b978-0-12-387685-0.00006-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Dnmt1, the principal DNA methyltransferase in mammalian cells, is a large and a highly dynamic enzyme with multiple regulatory features that can control DNA methylation in cells. This chapter highlights how insights into Dnmt1 structure and function can advance our understanding of DNA methylation in cells. The allosteric site(s) on Dnmt1 can regulate processes of de novo and maintenance DNA methylation in cells. Remaining open questions include which molecules, by what mechanism, bind at the allosteric site(s) in cells? Different phosphorylation sites on Dnmt1 can change its activity or ability to bind DNA target sites. Thirty-one different molecules are currently known to have physical and/or functional interaction with Dnmt1 in cells. The Dnmt1 structure and enzymatic mechanism offer unique insights into those interactions. The interacting molecules are involved in chromatin organization, DNA repair, cell cycle regulation, and apoptosis and also include RNA polymerase II, some RNA-binding proteins, and some specific Dnmt1-inhibitory RNA molecules. Combined insights from studies of different enzymatic features of Dnmt1 offer novel ideas for development of drug candidates, and can be used in selection of promising drug candidates from more than 15 different compounds that have been identified as possible inhibitors of DNA methylation in cells.
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Affiliation(s)
- Željko M Svedružić
- Medical Biochemistry, PB Rab, Faculty of Medicine, University of Rijeka, Rab, Croatia
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20
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Kaushal PS, Talawar RK, Varshney U, Vijayan M. Structure of uracil-DNA glycosylase from Mycobacterium tuberculosis: insights into interactions with ligands. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:887-92. [PMID: 20693660 PMCID: PMC2917283 DOI: 10.1107/s1744309110023043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 06/15/2010] [Indexed: 11/10/2022]
Abstract
Uracil N-glycosylase (Ung) is the most thoroughly studied of the group of uracil DNA-glycosylase (UDG) enzymes that catalyse the first step in the uracil excision-repair pathway. The overall structure of the enzyme from Mycobacterium tuberculosis is essentially the same as that of the enzyme from other sources. However, differences exist in the N- and C-terminal stretches and some catalytic loops. Comparison with appropriate structures indicate that the two-domain enzyme closes slightly when binding to DNA, while it opens slightly when binding to the proteinaceous inhibitor Ugi. The structural changes in the catalytic loops on complexation reflect the special features of their structure in the mycobacterial protein. A comparative analysis of available sequences of the enzyme from different sources indicates high conservation of amino-acid residues in the catalytic loops. The uracil-binding pocket in the structure is occupied by a citrate ion. The interactions of the citrate ion with the protein mimic those of uracil, in addition to providing insights into other possible interactions that inhibitors could be involved in.
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Affiliation(s)
- Prem Singh Kaushal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ramappa K. Talawar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - M. Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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21
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Zharkov DO, Mechetin GV, Nevinsky GA. Uracil-DNA glycosylase: Structural, thermodynamic and kinetic aspects of lesion search and recognition. Mutat Res 2010; 685:11-20. [PMID: 19909758 PMCID: PMC3000906 DOI: 10.1016/j.mrfmmm.2009.10.017] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2009] [Revised: 10/24/2009] [Accepted: 10/29/2009] [Indexed: 11/19/2022]
Abstract
Uracil appears in DNA as a result of cytosine deamination and by incorporation from the dUTP pool. As potentially mutagenic and deleterious for cell regulation, uracil must be removed from DNA. The major pathway of its repair is initiated by uracil-DNA glycosylases (UNG), ubiquitously found enzymes that hydrolyze the N-glycosidic bond of deoxyuridine in DNA. This review describes the current understanding of the mechanism of uracil search and recognition by UNG. The structure of UNG proteins from several species has been solved, revealing a specific uracil-binding pocket located in a DNA-binding groove. DNA in the complex with UNG is highly distorted to allow the extrahelical recognition of uracil. Thermodynamic studies suggest that UNG binds with appreciable affinity to any DNA, mainly due to the interactions with the charged backbone. The increase in the affinity for damaged DNA is insufficient to account for the exquisite specificity of UNG for uracil. This specificity is likely to result from multistep lesion recognition process, in which normal bases are rejected at one or several pre-excision stages of enzyme-substrate complex isomerization, and only uracil can proceed to enter the active site in a catalytically competent conformation. Search for the lesion by UNG involves random sliding along DNA alternating with dissociation-association events and partial eversion of undamaged bases for initial sampling.
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Affiliation(s)
- Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
- Department of Molecular Biology, Faculty of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Grigory V. Mechetin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Georgy A. Nevinsky
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
- Department of Molecular Biology, Faculty of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
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22
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Impact of linker strain and flexibility in the design of a fragment-based inhibitor. Nat Chem Biol 2009; 5:407-13. [PMID: 19396178 PMCID: PMC3178264 DOI: 10.1038/nchembio.163] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 02/23/2009] [Indexed: 11/21/2022]
Abstract
The linking together of molecular fragments that bind to adjacent sites on an enzyme can lead to high affinity inhibitors. Ideally, this strategy would employ linkers that do not perturb the optimal binding geometries of the fragments and do not have excessive conformational flexibility that would increase the entropic penalty of binding. In reality, these aims are seldom realized due to limitations in linker chemistry. Here we systematically explore the energetic and structural effects of rigid and flexible linkers on the binding of a fragment-based inhibitor of human uracil DNA glycosylase. Analysis of the free energies of binding in combination with co-crystal structures shows that the flexibility and strain of a given linker can have a significant impact on binding affinity even when the binding fragments are optimally positioned. Such effects are not apparent from inspection of structures and underscore the importance of linker optimization in fragment-based drug discovery efforts.
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23
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Huang H, Stivers JT, Greenberg MM. Competitive inhibition of uracil DNA glycosylase by a modified nucleotide whose triphosphate is a substrate for DNA polymerase. J Am Chem Soc 2009; 131:1344-5. [PMID: 19173657 DOI: 10.1021/ja807705z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Base excision repair (BER) enzymes are attractive targets for antiviral and anticancer agents. A number of nucleotides and nucleotide analogues are potent competitive inhibitors of BER glycosylases when they are incorporated into synthetic oligonucleotides. However, these molecules often are not substrates for DNA polymerases, which limits their utility in cells and as potential therapeutic agents. 1'-Cyano-2'-deoxyuridine (CNdU) is a nanomolar competitive inhibitor of uracil DNA glycosylase. In addition, the respective nucleotide triphosphate is accepted as a substrate by the Klenow fragment (exo(-)) of DNA polymerase I from E. coli. This is the first competitive inhibitor of UDG that is incorporated into DNA by Klenow exo(-), a model replicative polymerase. 1'-Cyano-2'-deoxyuridine (CNdU) and related molecules may prove useful as a new family of therapeutic or experimental agents that target DNA repair by using the cells' polymerase(s) to incorporate them into DNA. A potential benefit of such a mechanism is that multiple incorporations can occur for longer DNA molecules leading to amplification of the inhibitory effect beyond that seen here with short DNA duplexes.
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Affiliation(s)
- Haidong Huang
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA
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24
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DNA polymerase bypass in vitro and in E. coli of a C-nucleotide analogue of Fapy-dG. Bioorg Med Chem 2008; 16:4029-34. [PMID: 18242999 DOI: 10.1016/j.bmc.2008.01.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Accepted: 01/14/2008] [Indexed: 11/20/2022]
Abstract
Bypass of the configurationally stable analogue (beta-C-Fapy x dG) of the formamidopyrimidine lesion derived from 2'-deoxyguanosine oxidation (Fapy x dG) was studied in vitro and in Escherichia coli. The exonuclease deficient Klenow fragment of E. coli DNA polymerase I (Klenow exo(-)) misincorporated dA most frequently opposite beta-C-Fapy x dG, but its efficiency was <0.2% of dC insertion. Klenow exo(-) fidelity was enhanced by the enzyme's high selectivity for extending duplexes only when dC was opposite beta-C-Fapy x dG. The expectations raised by these in vitro data were realized when beta-C-Fapy x dG replication was studied in E. coli by transfecting M13mp7(L2) bacteriophage DNA containing the nucleotide analogue within the lacZ gene in 4 local sequence contexts. The bypass efficiency of beta-C-Fapy x dG varied between 45% and 70% compared to a genome containing only native nucleotides. Mutation frequencies at the site of the lesions in the originally transfected genomes were determined using the REAP assay [Delaney, J. C.; Essigmann, J. M. Methods Enzymol.2006, 408, 1]. The levels of mutations could not be distinguished between those observed when genomes containing native nucleotides were replicated, indicating that the mutagenicity of beta-C-Fapy x dG was <1%. These data and previous reports indicate that beta-C-Fapy x dG is a good model of Fapy x dG in E. coli. In addition, these results and the previous report of beta-C-Fapy x dG binding to the base excision repair protein formamidopyrimidine glycosylase suggest that this analogue could be useful as a DNA repair inhibitor.
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25
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Seiple LA, Cardellina JH, Akee R, Stivers JT. Potent inhibition of human apurinic/apyrimidinic endonuclease 1 by arylstibonic acids. Mol Pharmacol 2007; 73:669-77. [PMID: 18042731 DOI: 10.1124/mol.107.042622] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Human apurinic/apyrimidinic endonuclease (Ape1) plays an important role by processing the >10,000 highly toxic abasic sites generated in the genome of each cell every day. Ape1 has recently emerged as a target for inhibition, in that its overexpression in tumors has been linked with poor response to both radiation and chemotherapy and lower overall patient survival. Inhibition of Ape1 using siRNA or the expression of a dominant-negative form of the protein has been shown to sensitize cells to DNA-damaging agents, including various chemotherapeutic agents. However, potent small-molecule inhibitors of Ape1 remain to be found. To this end, we screened Ape1 against the NCI Diversity Set of small molecules and discovered aromatic nitroso, carboxylate, sulfonamide, and arylstibonic acid compounds with micromolar affinities for the protein. A further screen of a 37-compound arylstibonic acid sublibrary identified ligands with IC(50) values in the range of 4 to 300 nM. The negatively charged stibonic acids act by a partial-mixed mode and probably serve as DNA phosphate mimics. These compounds provide a useful scaffold for development of chemotherapeutic agents against Ape1.
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Affiliation(s)
- Lauren A Seiple
- The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore MD 21205-2185, USA
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26
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Pettersen HS, Sundheim O, Gilljam KM, Slupphaug G, Krokan HE, Kavli B. Uracil-DNA glycosylases SMUG1 and UNG2 coordinate the initial steps of base excision repair by distinct mechanisms. Nucleic Acids Res 2007; 35:3879-92. [PMID: 17537817 PMCID: PMC1919486 DOI: 10.1093/nar/gkm372] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA glycosylases UNG and SMUG1 excise uracil from DNA and belong to the same protein superfamily. Vertebrates contain both SMUG1 and UNG, but their distinct roles in base excision repair (BER) of deaminated cytosine (U:G) are still not fully defined. Here we have examined the ability of human SMUG1 and UNG2 (nuclear UNG) to initiate and coordinate repair of U:G mismatches. When expressed in Escherichia coli cells, human UNG2 initiates complete repair of deaminated cytosine, while SMUG1 inhibits cell proliferation. In vitro, we show that SMUG1 binds tightly to AP-sites and inhibits AP-site cleavage by AP-endonucleases. Furthermore, a specific motif important for the AP-site product binding has been identified. Mutations in this motif increase catalytic turnover due to reduced product binding. In contrast, the highly efficient UNG2 lacks product-binding capacity and stimulates AP-site cleavage by APE1, facilitating the two first steps in BER. In summary, this work reveals that SMUG1 and UNG2 coordinate the initial steps of BER by distinct mechanisms. UNG2 is apparently adapted to rapid and highly coordinated repair of uracil (U:G and U:A) in replicating DNA, while the less efficient SMUG1 may be more important in repair of deaminated cytosine (U:G) in non-replicating chromatin.
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Affiliation(s)
| | | | | | | | | | - Bodil Kavli
- *To whom correspondence should be addressed. +47 72 573221+47 72576400
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