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Martella M, Pichiorri F, Chikhale RV, Abdelhamid MAS, Waller ZAE, Smith S. i-Motif formation and spontaneous deletions in human cells. Nucleic Acids Res 2022; 50:3445-3455. [PMID: 35253884 PMCID: PMC8989526 DOI: 10.1093/nar/gkac158] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 02/01/2022] [Accepted: 02/26/2022] [Indexed: 01/14/2023] Open
Abstract
Concatemers of d(TCCC) that were first detected through their association with deletions at the RACK7 locus, are widespread throughout the human genome. Circular dichroism spectra show that d(GGGA)n sequences form G-quadruplexes when n > 3, while i-motif structures form at d(TCCC)n sequences at neutral pH when n ≥ 7 in vitro. In the PC3 cell line, deletions are observed only when the d(TCCC)n variant is long enough to form significant levels of unresolved i-motif structure at neutral pH. The presence of an unresolved i-motif at a representative d(TCCC)n element at RACK7 was suggested by experiments showing that that the region containing the d(TCCC)9 element was susceptible to bisulfite attack in native DNA and that d(TCCC)9 oligo formed an i-motif structure at neutral pH. This in turn suggested that that the i-motif present at this site in native DNA must be susceptible to bisulfite mediated deamination even though it is a closed structure. Bisulfite deamination of the i-motif structure in the model oligodeoxynucleotide was confirmed using mass spectrometry analysis. We conclude that while G-quadruplex formation may contribute to spontaneous mutation at these sites, deletions actually require the potential for i-motif to form and remain unresolved at neutral pH.
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Affiliation(s)
- Marianna Martella
- Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Flavia Pichiorri
- Judy and Bernard Briskin Center for Multiple Myeloma Research, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
| | - Rupesh V Chikhale
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Mahmoud A S Abdelhamid
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Zoë A E Waller
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Steven S Smith
- Department of Hematologic Malignancies Translational Science, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
- Beckman Research Institute of the City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010, USA
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2
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Vucicevic J, Nikolic K, Mitchell JB. Rational Drug Design of Antineoplastic Agents Using 3D-QSAR, Cheminformatic, and Virtual Screening Approaches. Curr Med Chem 2019; 26:3874-3889. [DOI: 10.2174/0929867324666170712115411] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/06/2017] [Accepted: 06/13/2017] [Indexed: 01/07/2023]
Abstract
Background:Computer-Aided Drug Design has strongly accelerated the development of novel antineoplastic agents by helping in the hit identification, optimization, and evaluation.Results:Computational approaches such as cheminformatic search, virtual screening, pharmacophore modeling, molecular docking and dynamics have been developed and applied to explain the activity of bioactive molecules, design novel agents, increase the success rate of drug research, and decrease the total costs of drug discovery. Similarity, searches and virtual screening are used to identify molecules with an increased probability to interact with drug targets of interest, while the other computational approaches are applied for the design and evaluation of molecules with enhanced activity and improved safety profile.Conclusion:In this review are described the main in silico techniques used in rational drug design of antineoplastic agents and presented optimal combinations of computational methods for design of more efficient antineoplastic drugs.
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Affiliation(s)
- Jelica Vucicevic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - John B.O. Mitchell
- EaStCHEM School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, United Kingdom
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Lamparska K, Clark J, Babilonia G, Bedell V, Yip W, Smith SS. 2'-Deoxyriboguanylurea, the primary breakdown product of 5-aza-2'-deoxyribocytidine, is a mutagen, an epimutagen, an inhibitor of DNA methyltransferases and an inducer of 5-azacytidine-type fragile sites. Nucleic Acids Res 2012; 40:9788-801. [PMID: 22850746 PMCID: PMC3479176 DOI: 10.1093/nar/gks706] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
5-Aza-2′-deoxycytidine (5azaC-dR) has been employed as an inhibitor of DNA methylation, a chemotherapeutic agent, a clastogen, a mutagen, an inducer of fragile sites and a carcinogen. However, its effects are difficult to quantify because it rapidly breaks down in aqueous solution to the stable compound 2′-deoxyriboguanylurea (GuaUre-dR). Here, we used a phosphoramidite that permits the introduction of GuaUre-dR at defined positions in synthetic oligodeoxynucleotides to demonstrate that it is a potent inhibitor of human DNA methyltransferase 1 (hDNMT1) and the bacterial DNA methyltransferase (M.EcoRII) and that it is a mutagen that can form productive base pairs with either Guanine or Cytosine. Pure GuaUre-dR was found to be an effective demethylating agent and was able to induce 5azaC-dR type fragile sites FRA1J and FRA9E in human cells. Moreover, we report that demethylation associated with C:G → G:C transversion and C:G → T:A transition mutations was observed in human cells exposed to pure GuaUre-dR. The data suggest that most of the effects attributed to 5azaC-dR are exhibited by its stable primary breakdown product.
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Affiliation(s)
- Katarzyna Lamparska
- Beckman Research Institute and Division of Urology and Urologic Oncology, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010-3000, USA
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Dyachenko OV, Schevchuk TV, Kretzner L, Buryanov YI, Smith SS. Human non-CG methylation: are human stem cells plant-like? Epigenetics 2010; 5:569-72. [PMID: 20647766 DOI: 10.4161/epi.5.7.12702] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Non-CG methylation is well characterized in plants, where it appears to play a role in gene silencing and genomic imprinting. Although strong evidence for the presence of non-CG methylation in animals has been available for some time, both its origin and function remain elusive. In this review we discuss available evidence on non-CG methylation in animals in light of evidence suggesting that the human stem cell methylome contains significant levels of methylation outside the CG site.
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Affiliation(s)
- Olga V Dyachenko
- Pushchino Branch, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia
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Champion C, Guianvarc'h D, Sénamaud-Beaufort C, Jurkowska RZ, Jeltsch A, Ponger L, Arimondo PB, Guieysse-Peugeot AL. Mechanistic insights on the inhibition of c5 DNA methyltransferases by zebularine. PLoS One 2010; 5:e12388. [PMID: 20808780 PMCID: PMC2927531 DOI: 10.1371/journal.pone.0012388] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 07/03/2010] [Indexed: 12/22/2022] Open
Abstract
In mammals DNA methylation occurs at position 5 of cytosine in a CpG context and regulates gene expression. It plays an important role in diseases and inhibitors of DNA methyltransferases (DNMTs)—the enzymes responsible for DNA methylation—are used in clinics for cancer therapy. The most potent inhibitors are 5-azacytidine and 5-azadeoxycytidine. Zebularine (1-(β-D-ribofuranosyl)-2(1H)- pyrimidinone) is another cytidine analog described as a potent inhibitor that acts by forming a covalent complex with DNMT when incorporated into DNA. Here we bring additional experiments to explain its mechanism of action. First, we observe an increase in the DNA binding when zebularine is incorporated into the DNA, compared to deoxycytidine and 5-fluorodeoxycytidine, together with a strong decrease in the dissociation rate. Second, we show by denaturing gel analysis that the intermediate covalent complex between the enzyme and the DNA is reversible, differing thus from 5-fluorodeoxycytidine. Third, no methylation reaction occurs when zebularine is present in the DNA. We confirm that zebularine exerts its demethylation activity by stabilizing the binding of DNMTs to DNA, hindering the methylation and decreasing the dissociation, thereby trapping the enzyme and preventing turnover even at other sites.
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Affiliation(s)
| | - Dominique Guianvarc'h
- Laboratoire des Biomolécules, UPMC Université Paris 06, CNRS, ENS, FR, Paris, France
| | | | - Renata Z. Jurkowska
- Jacobs University Bremen, School of Engineering and Science, Bremen, Germany
| | - Albert Jeltsch
- Jacobs University Bremen, School of Engineering and Science, Bremen, Germany
| | - Loïc Ponger
- MNHN CNRS UMR7196, Paris, France
- INSERM U565, Paris, France
| | - Paola B. Arimondo
- MNHN CNRS UMR7196, Paris, France
- INSERM U565, Paris, France
- * E-mail: (PBA); (ALGP)
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Shieh FK, Reich NO. AdoMet-dependent Methyl-transfer: Glu119 Is Essential for DNA C5-Cytosine Methyltransferase M.HhaI. J Mol Biol 2007; 373:1157-68. [PMID: 17897676 DOI: 10.1016/j.jmb.2007.08.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2007] [Revised: 07/17/2007] [Accepted: 08/03/2007] [Indexed: 11/21/2022]
Abstract
The role of Glu119 in S-adenosyl-L-methionine-dependent DNA methyltransferase M.HhaI-catalyzed DNA methylation was studied. Glu119 belongs to the highly conserved Glu/Asn/Val motif found in all DNA C5-cytosine methyltransferases, and its importance for M.HhaI function remains untested. We show that formation of the covalent intermediate between Cys81 and the target cytosine requires Glu119, since conversion to Ala, Asp or Gln lowers the rate of methyl transfer 10(2)-10(6) fold. Further, unlike the wild-type M.HhaI, these mutants are not trapped by the substrate in which the target cytosine is replaced with the mechanism-based inhibitor 5-fluorocytosine. The DNA binding affinity for the Glu119Asp mutant is decreased 10(3)-fold. Thus, the ability of the enzyme to stabilize the extrahelical cytosine is coupled directly to tight DNA binding. The structures of the ternary protein/DNA/AdoHcy complexes for both the Glu119Ala and Glu119Gln mutants (2.70 A and 2.75 A, respectively) show that the flipped base is positioned nearly identically with that observed in the wild-type M.HhaI complex. A single water molecule in the Glu119Ala structure between Ala119 and the extrahelical cytosine N3 is lacking in the Glu119Gln and wild-type M.HhaI structures, and most likely accounts for this mutant's partial activity. Glu119 has essential roles in activating the target cytosine for nucleophilic attack and contributes to tight DNA binding.
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Affiliation(s)
- Fa-Kuen Shieh
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
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Shevchuk T, Kretzner L, Munson K, Axume J, Clark J, Dyachenko OV, Caudill M, Buryanov Y, Smith SS. Transgene-induced CCWGG methylation does not alter CG methylation patterning in human kidney cells. Nucleic Acids Res 2005; 33:6124-36. [PMID: 16246913 PMCID: PMC1266073 DOI: 10.1093/nar/gki920] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2005] [Revised: 09/09/2005] [Accepted: 10/05/2005] [Indexed: 12/21/2022] Open
Abstract
Several reports suggest that C(m)CWGG methylation tends not to co-exist with (m)CG methylation in human cells. We have asked whether or not methylation at CCWGG sites can influence CG methylation. DNA from cells expressing an M.EcoRII-GFP fusion was actively methylated at CCWGG sites. CG methylation as measured by R.HpaII/R.MspI ratios was unchanged in cells expressing the transgene. Cloned representatives of C(m)CWGG methylated DNA often contained, or were adjacent to an ALU repeat, suggesting that M.EcoRII-GFP actively methylated gene-rich R-band DNA. The transgenic methyltransferase applied C(m)CWGG methylation to a representative human promoter that was heavily methylated at CG dinucleotides (the SERPINB5 promoter) and to a representative promoter that was essentially unmethylated at CG dinucleotides (the APC promoter). In each case, the CG methylation pattern remained in its original state, unchanged by the presence of neighboring C(m)CWGG sites. Q-PCR measurements showed that RNA expression from the APC gene was not significantly altered by the presence of C(m)CWGG in its promoter. Kinetic studies suggested that an adjacent C(m)CWGG methylation site influences neither the maintenance nor the de novo methylation activities of purified human Dnmt1. We conclude that C(m)CWGG methylation does not exert a significant effect on CG methylation in human kidney cells.
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Affiliation(s)
- Taras Shevchuk
- City of Hope National Medical Center and Beckman Research Institute1500 E. Duarte Road, Duarte, CA 91010, USA
- Laboratory of Plant Biotechnology, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesPushchino, Moscow Region 142290, Russia
| | - Leo Kretzner
- City of Hope National Medical Center and Beckman Research Institute1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Kristofer Munson
- City of Hope National Medical Center and Beckman Research Institute1500 E. Duarte Road, Duarte, CA 91010, USA
| | - John Axume
- Department of Human Nutrition and Food Science, College of Agriculture, California State Polytechnic University3801 West Temple Avenue, Pomona, CA 91768, USA
| | - Jarrod Clark
- City of Hope National Medical Center and Beckman Research Institute1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Olga V. Dyachenko
- Laboratory of Plant Biotechnology, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesPushchino, Moscow Region 142290, Russia
| | - Marie Caudill
- Department of Human Nutrition and Food Science, College of Agriculture, California State Polytechnic University3801 West Temple Avenue, Pomona, CA 91768, USA
| | - Yaroslav Buryanov
- Laboratory of Plant Biotechnology, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesPushchino, Moscow Region 142290, Russia
| | - Steven S. Smith
- City of Hope National Medical Center and Beckman Research Institute1500 E. Duarte Road, Duarte, CA 91010, USA
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Vilkaitis G, Suetake I, Klimasauskas S, Tajima S. Processive Methylation of Hemimethylated CpG Sites by Mouse Dnmt1 DNA Methyltransferase. J Biol Chem 2005; 280:64-72. [PMID: 15509558 DOI: 10.1074/jbc.m411126200] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA methyltransferase Dnmt1 ensures clonal transmission of lineage-specific DNA methylation patterns in a mammalian genome during replication. Dnmt1 is targeted to replication foci, interacts with PCNA, and favors methylating the hemimethylated form of CpG sites. To understand the underlying mechanism of its maintenance function, we purified recombinant forms of full-length Dnmt1, a truncated form of Dnmt1-(291-1620) lacking the binding sites for PCNA and DNA and examined their processivity using a series of long unmethylated and hemimethylated DNA substrates. Direct analysis of methylation patterns using bisulfite-sequencing and hairpin-PCR techniques demonstrated that full-length Dnmt1 methylates hemimethylated DNA with high processivity and a fidelity of over 95%, but unmethylated DNA with much less processivity. The truncated form of Dnmt1 showed identical properties to full-length Dnmt1 indicating that the N-terminal 290-amino acid residue region of Dnmt1 is not required for preferential activity toward hemimethylated sites or for processivity of the enzyme. Remarkably, our analyses also revealed that Dnmt1 methylates hemimethylated CpG sites on one strand of double-stranded DNA during a single processive run. Our findings suggest that these inherent enzymatic properties of Dnmt1 play an essential role in the faithful and efficient maintenance of methylation patterns in the mammalian genome.
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Affiliation(s)
- Giedrius Vilkaitis
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
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