1
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Snodin DJ, Trejo-Martin A, Ponting DJ, Smith GF, Czich A, Cross K, Custer L, Elloway J, Greene N, Kalgutkar AS, Stalford SA, Tennant RE, Vock E, Zalewski A, Ziegler V, Dobo KL. Mechanisms of Nitrosamine Mutagenicity and Their Relationship to Rodent Carcinogenic Potency. Chem Res Toxicol 2024; 37:181-198. [PMID: 38316048 DOI: 10.1021/acs.chemrestox.3c00327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
A thorough literature review was undertaken to understand how the pathways of N-nitrosamine transformation relate to mutagenic potential and carcinogenic potency in rodents. Empirical and computational evidence indicates that a common radical intermediate is created by CYP-mediated hydrogen abstraction at the α-carbon; it is responsible for both activation, leading to the formation of DNA-reactive diazonium species, and deactivation by denitrosation. There are competing sites of CYP metabolism (e.g., β-carbon), and other reactive species can form following initial bioactivation, although these alternative pathways tend to decrease rather than enhance carcinogenic potency. The activation pathway, oxidative dealkylation, is a common reaction in drug metabolism and evidence indicates that the carbonyl byproduct, e.g., formaldehyde, does not contribute to the toxic properties of N-nitrosamines. Nitric oxide (NO), a side product of denitrosation, can similarly be discounted as an enhancer of N-nitrosamine toxicity based on carcinogenicity data for substances that act as NO-donors. However, not all N-nitrosamines are potent rodent carcinogens. In a significant number of cases, there is a potency overlap with non-N-nitrosamine carcinogens that are not in the Cohort of Concern (CoC; high-potency rodent carcinogens comprising aflatoxin-like-, N-nitroso-, and alkyl-azoxy compounds), while other N-nitrosamines are devoid of carcinogenic potential. In this context, mutagenicity is a useful surrogate for carcinogenicity, as proposed in the ICH M7 (R2) (2023) guidance. Thus, in the safety assessment and control of N-nitrosamines in medicines, it is important to understand those complementary attributes of mechanisms of mutagenicity and structure-activity relationships that translate to elevated potency versus those which are associated with a reduction in, or absence of, carcinogenic potency.
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Affiliation(s)
| | - Alejandra Trejo-Martin
- Gilead Sciences Inc. Nonclinical Safety and Pathobiology (NSP), Foster City, California 94404, United States
| | | | - Graham F Smith
- AstraZeneca, Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, Research and Development, CB2 0AA Cambridge, U.K
| | - Andreas Czich
- Sanofi, Research and Development, Preclinical Safety, 65926 Frankfurt, Germany
| | - Kevin Cross
- Instem, Conshohocken, Pennsylvania 19428, United States
| | - Laura Custer
- Bristol-Myers Squibb, Nonclinical Safety, New Brunswick, New Jersey 08903, United States
| | - Joanne Elloway
- AstraZeneca, Safety Sciences, Clinical Pharmacology and Safety Sciences Research and Development, CB2 0AA Cambridge, U.K
| | - Nigel Greene
- AstraZeneca, Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, Research and Development, Waltham, Massachusetts 02451, United States
| | - Amit S Kalgutkar
- Medicine Design, Pfizer Worldwide Research, Development, and Medical, Cambridge, Massachusetts 02139, United States
| | | | | | - Esther Vock
- Boehringer-Ingelheim Pharma GmbH & Co., KG, 88397 Biberach an der Riss, Germany
| | - Adam Zalewski
- Bayer AG, Pharmaceuticals, Genetic and Computational Toxicology, 13342 Berlin, Germany
| | - Verena Ziegler
- Bayer AG, Pharmaceuticals, Genetic and Computational Toxicology, 13342 Berlin, Germany
| | - Krista L Dobo
- Drug Safety Research and Development, Global Portfolio and Regulatory Strategy, Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
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2
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Wenzel J, Schmidt F, Blumrich M, Amberg A, Czich A. Predicting DNA-Reactivity of N-Nitrosamines: A Quantum Chemical Approach. Chem Res Toxicol 2022; 35:2068-2084. [PMID: 36302168 DOI: 10.1021/acs.chemrestox.2c00217] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
N-Nitrosamines (NAs) are a class of reactive organic chemicals that humans may be exposed to from environmental sources, food but also impurities in pharmaceutical preparations. Some NAs were identified as DNA-reactive mutagens and many of those have been classified as probable human carcinogens. Beyond high-potency mutagenic carcinogens that need to be strictly controlled, NAs of low potency need to be considered for risk assessment as well. NA impurities and nitrosylated products of active pharmaceutical ingredients (APIs) often arise from production processes or degradation. Most NAs require metabolic activation to ultimately become carcinogens, and their activation can be appropriately described by first-principles computational chemistry approaches. To this end, we treat NA-induced DNA alkylation as a series of subsequent association and dissociation reaction steps that can be calculated stringently by density functional theory (DFT), including α-hydroxylation, proton transfer, hydroxyl elimination, direct SN2/SNAr DNA alkylation, competing hydrolysis and SN1 reactions. Both toxification and detoxification reactions are considered. The activation reactions are modeled by DFT at a high level of theory with an appropriate solvent model to compute Gibbs free energies of the reactions (thermodynamical effects) and activation barriers (kinetic effects). We study congeneric series of aliphatic and cyclic NAs to identify trends. Overall, this work reveals detailed insight into mechanisms of activation for NAs, suggesting that individual steric and electronic factors have directing and rate-determining influence on the formation of carbenium ions as the ultimate pro-mutagens and thus carcinogens. Therefore, an individual risk assessment of NAs is suggested, as exemplified for the complex API-like 4-(N-nitroso-N-methyl)aminoantipyrine which is considered as low-potency NA by in silico prediction.
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Affiliation(s)
- Jan Wenzel
- Sanofi, R&D, Preclinical Safety, Industriepark Höchst, Industriepark Höchst, 65926Frankfurt am Main, Germany
| | - Friedemann Schmidt
- Sanofi, R&D, Preclinical Safety, Industriepark Höchst, Industriepark Höchst, 65926Frankfurt am Main, Germany
| | - Matthias Blumrich
- Sanofi, R&D, Preclinical Safety, Industriepark Höchst, Industriepark Höchst, 65926Frankfurt am Main, Germany
| | - Alexander Amberg
- Sanofi, R&D, Preclinical Safety, Industriepark Höchst, Industriepark Höchst, 65926Frankfurt am Main, Germany
| | - Andreas Czich
- Sanofi, R&D, Preclinical Safety, Industriepark Höchst, Industriepark Höchst, 65926Frankfurt am Main, Germany
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3
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Sengupta S, Das P. Application of diazonium chemistry in purine modifications: A focused review. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Saumitra Sengupta
- Department of Chemistry Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Parthasarathi Das
- Department of Chemistry Indian Institute of Technology (Indian School of Mines) Dhanbad India
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4
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Vongsutilers V, Gannett PM. C8-Guanine modifications: effect on Z-DNA formation and its role in cancer. Org Biomol Chem 2018. [DOI: 10.1039/c8ob00030a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Participation of Z DNA in normal and disease related biological processes.
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Affiliation(s)
- V. Vongsutilers
- Department of Food and Pharmaceutical Chemistry
- Faculty of Pharmaceutical Sciences
- Chulalongkorn University
- Thailand
| | - P. M. Gannett
- College of Pharmacy
- Nova Southeastern University
- Ft. Lauderdale
- USA
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5
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Manderville RA, Wetmore SD. Mutagenicity of Ochratoxin A: Role for a Carbon-Linked C8-Deoxyguanosine Adduct? JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:7097-7105. [PMID: 28830149 DOI: 10.1021/acs.jafc.6b03897] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Ochratoxin A (OTA) is a fungal toxin that is considered to be a potent kidney carcinogen in rodent models. The toxin produces double strand breaks and has a propensity for deletions, single-base substitutions, and insertions. The toxin reacts covalently with DNA to afford a C8-2'-deoxyguanosine carbon-linked adduct (OT-dG) as the major lesion in animal tissues. Incorporation of model C-linked C8-aryl-dG adducts into the G3 site of the NarI sequence demonstrates a tendency to induce base substitutions and deletion mutations in primer extension assays using model polymerases. The degree of misincorporation induced by the C-linked C8-dG adducts correlates with an ability to adopt the promutagenic syn conformation within the NarI duplex as predicted by molecular dynamics (MD) simulations. MD simulations of the OT-dG adduct within the NarI duplex predict an even greater degree of conformational flexibility, suggesting enhanced in vitro mutagenicity compared to the simpler model C-linked C8-dG adducts. Together these findings support the role of OT-dG in promoting OTA-mediated mutagenicity and carcinogenicity in animal studies.
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Affiliation(s)
- Richard A Manderville
- Departments of Chemistry and Toxicology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
| | - Stacey D Wetmore
- Department of Chemistry & Biochemistry, University of Lethbridge , Lethbridge, Alberta, Canada T1K 3M4
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6
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Manderville RA, Wetmore SD. Understanding the Mutagenicity of O-Linked and C-Linked Guanine DNA Adducts: A Combined Experimental and Computational Approach. Chem Res Toxicol 2016; 30:177-188. [DOI: 10.1021/acs.chemrestox.6b00323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Richard A. Manderville
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Stacey D. Wetmore
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, AB, Canada T1K 3M4
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7
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Sharma P, Majdi Yazdi M, Merriman A, Manderville RA, Wetmore SD. Influence of the Linkage Type and Functional Groups in the Carcinogenic Moiety on the Conformational Preferences of Damaged DNA: Structural and Energetic Characterization of Carbon- and Oxygen-Linked C8-Phenolic-Guanine Adducts. Chem Res Toxicol 2015; 28:782-96. [DOI: 10.1021/tx500527p] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Purshotam Sharma
- Department
of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Mohadeseh Majdi Yazdi
- Department
of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Ashlyn Merriman
- Department
of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Richard A. Manderville
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, Ontario, Canada N1G2W1
| | - Stacey D. Wetmore
- Department
of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
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8
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Sharma P, Manderville RA, Wetmore SD. Modeling the conformational preference of the carbon-bonded covalent adduct formed upon exposure of 2'-deoxyguanosine to ochratoxin A. Chem Res Toxicol 2013; 26:803-16. [PMID: 23560542 DOI: 10.1021/tx4000864] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The conformational flexibility of the C8-linked guanine adduct formed from attachment of ochratoxin A (OTA) was analyzed using a systematic computational approach and models ranging from the nucleobase to the adducted DNA helix. A focus was placed on the influence of the C8-modification of 2'-deoxyguanosine (dG) on the preferred relative arrangement of the nucleobase and the C8-substituent and, more importantly, the anti/syn conformational preference with respect to the glycosidic bond. Although OTA is twisted with respect to the base in the nucleobase model, addition of the deoxyribose sugar induces a further twist and restricts rotation about the C-C linkage due to close contacts between OTA and the sugar. The nucleoside model preferentially adpots a syn orientation (by 10-20 kJ mol(-1) depending on the OTA conformation) due to the presence of an O5'-H···N3 interaction. However, when this hydrogen bond is eliminated, which better mimics the DNA environment, a small (<5 kJ mol(-1)) anti/syn energy difference is predicted. Inclusion of the 5'-monophosphate group leads to an up to 20 kJ mol(-1) preference for the syn (nucleotide) conformation due to stabilizing base-phosphate interactions involving the amino group of guanine. Nevertheless, MD simulations and free energy analysis predict that both syn- and anti-conformations of OTB-dG are equally stable in helices when paired opposite cytosine. These results indicate that the adduct will likely adopt a syn conformation in an isolated nucleoside and nucleotide, while a mixture of syn and anti conformations will be observed in DNA duplexes. Since the syn conformation could stabilize base mismatches upon DNA replication or Z-DNA structures with varied biological outcomes, future computational and experimental work should elucidate the consequences of the conformational preference of this potentially harmful DNA lesion.
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Affiliation(s)
- Purshotam Sharma
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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C8-linked bulky guanosine DNA adducts: experimental and computational insights into adduct conformational preferences and resulting mutagenicity. Future Med Chem 2012; 4:1981-2007. [PMID: 23088278 DOI: 10.4155/fmc.12.138] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bulky DNA adducts are formed through the covalent attachment of aryl groups to the DNA nucleobases. Many of these adducts are known to possess conformational heterogeneity, which is responsible for the variety of mutagenic outcomes associated with these lesions. The present contribution reviews several conformational and mutagenic themes that are prevalent among the DNA adducts formed at the C8-site of the guanine nucleobase. The most important conclusions obtained (to date) from experiments are summarized including the anti/syn conformational preference of the adducts, their potential to inflict DNA mutations and mismatch stabilization, and their interactions with DNA polymerases and repair enzymes. Additionally, the unique role that computer calculations can play in understanding the structural properties of these adducts are highlighted.
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10
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Millen AL, Kamenz BL, Leavens FMV, Manderville RA, Wetmore SD. Conformational flexibility of C8-phenoxylguanine adducts in deoxydinucleoside monophosphates. J Phys Chem B 2011; 115:12993-3002. [PMID: 21942470 DOI: 10.1021/jp2057332] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
M06-2X/6-31G(d,p) is used to calculate the structure of all natural deoxydinucleoside monophosphates with G in the 5' or 3' position, the anti or syn conformation, and each natural (A, C, G, T) base in the corresponding flanking position. When the ortho or para C8-phenoxyl-2'-deoxyguanosine (C8-phenoxyl-dG) adduct replaces G in each model, there is little change in the relative base-base orientation or backbone conformation. However, the orientation of the C8-phenoxyl group can be characterized according to the position (5' versus 3'), conformation (anti versus syn), and isomer (ortho versus para) of damage. Although the degree of coplanarity between the phenoxyl ring and G base in the ortho adduct is highly affected by the sequence since the hydroxyl group can interact with neighboring bases, the para adduct generally does not exhibit discrete interactions with flanking bases. For both adducts, steric clashes between the phenoxyl group and the backbone or flanking base destabilize the anti conformation preferred by the natural nucleotide and thereby result in a clear preference for the syn conformation regardless of the sequence or position. This contrasts the conclusions drawn from smaller (nucleoside, nucleotide) models previously used in the literature, which stresses the importance of using models that address the steric constraints present due to the surrounding environment. Since replication errors for other C8-dG bulky adducts have been linked to a preference for the syn conformation, our findings provide insight into the possible mutagenicity of phenolic adducts.
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Affiliation(s)
- Andrea L Millen
- Department of Chemistry, University of Lethbridge, Lethbridge, Alberta, Canada
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11
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Sagoo S, Beach DG, Manderville RA, Gabryelski W. Tautomerization in gas-phase ion chemistry of isomeric C-8 deoxyguanosine adducts from phenol-induced DNA damage. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:41-9. [PMID: 21184435 DOI: 10.1002/jms.1869] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Collision-induced dissociation (CID) of 8-(4''-hydroxyphenyl)-2'-deoxyguanosine and 8-(2''-hydroxyphenyl)-2'-deoxyguanosine was investigated using sequential tandem mass spectrometry. These adducts represent biomarkers of DNA damage linked to phenolic radicals and were investigated to gain insight into the effects of chemical structure of a C-8 modification on fragmentation pathways of modified 2'-deoxyguanosine (dG). CID in MS(2) of the deprotonated molecules of both the isomers generated the same product ion having the same m/z values. CID in MS(3) of the product ion at m/z 242 and CID in MS(4) experiments carried out on the selected product ions at m/z 225 and m/z 218 afford distinct fragmentation patterns. The conformational properties of isomeric product ions from CID showed that the ortho-isomers possess the unique ability to tautomerize through an intramolecular proton transfer between the phenolic OH group and the imine nitrogen (N7). Tautomerization of ortho-isomers to their keto-tautomers led to differences in their system of conjugated double bonds compared with either their enol-tautomer or the para-isomer. The charge redistribution through the N-7 site on the imidazole ring is a critical step in guanosine adduct fragmentation which is disrupted by the formation of the keto-tautomer. For this reason, different reaction pathways are observed for 8-(4''-hydroxyphenyl)-2'-deoxyguanosine and 8-(2''-hydroxyphenyl)-2'-deoxyguanosine. We present herein the dissociation and the gas-phase ion-molecule reactions for highly conjugated ions involved in the CID ion chemistry of the investigated adducts. These will be useful for those using tandem mass spectrometry for structural elucidation of C-8 modified dG adducts. This study demonstrates that the modification at the C-8 site of dG has the potential to significantly alter the reactivity of adducts. We also show the ability of tandem mass spectrometry to completely differentiate between the isomeric dG adducts investigated.
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Affiliation(s)
- Sandeep Sagoo
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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12
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Omumi A, Beach DG, Baker M, Gabryelski W, Manderville RA. Postsynthetic guanine arylation of DNA by Suzuki-Miyaura cross-coupling. J Am Chem Soc 2010; 133:42-50. [PMID: 21067186 DOI: 10.1021/ja106158b] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Direct radical addition reactions at the C(8)-site of 2'-deoxyguanosine (dG) can afford C(8)-Ar-dG adducts that are produced by carcinogenic arylhydrazines, polycyclic aromatic hydrocarbons, and certain phenolic toxins. Such modified nucleobases are also highly fluorescent for sensing applications and possess useful electron transfer properties. The site-specific synthesis of oligonucleotides containing the C(8)-Ar-G adduct can be problematic. These lesions are sensitive to acids and oxidants that are commonly used in solid-phase DNA synthesis and are too bulky to be accepted as substrates for enzymatic synthesis by DNA polymerases. Using the Suzuki-Miyaura cross-coupling reaction, we have synthesized a number of C(8)-Ar-G-modified oligonucleotides (dimers, trimers, decamers, and a 15-mer) using a range of arylboronic acids. Good to excellent yields were obtained, and the reaction is insensitive to the nature of the bases flanking the convertible 8-Br-G nucleobase, as both pyrimidines and purines are tolerated. The impact of the C(8)-Ar-G lesion was also characterized by electrospray ionization tandem mass spectrometry, UV melting temperature analysis, circular dichroism, and fluorescence spectroscopy. The C(8)-Ar-G-modified oligonucleotides are expected to be useful substrates for diagnostic applications and understanding the biological impact of the C(8)-Ar-G lesion.
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Affiliation(s)
- Alireza Omumi
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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13
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Millen AL, Churchill CDM, Manderville RA, Wetmore SD. Effect of Watson−Crick and Hoogsteen Base Pairing on the Conformational Stability of C8-Phenoxyl-2′-deoxyguanosine Adducts. J Phys Chem B 2010; 114:12995-3004. [DOI: 10.1021/jp105817p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Andrea L. Millen
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Cassandra D. M. Churchill
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Richard A. Manderville
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Stacey D. Wetmore
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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Shim EJ, Przybylski JL, Wetmore SD. Effects of nucleophile, oxidative damage, and nucleobase orientation on the glycosidic bond cleavage in deoxyguanosine. J Phys Chem B 2010; 114:2319-26. [PMID: 20095611 DOI: 10.1021/jp9113656] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deglycosylation of nucleotides occurs during many essential biological processes, including DNA repair, and is initiated by a variety of nucleophiles. In the present work, density functional theory (B3LYP) was used to investigate the thermodynamics and kinetics of the glycosidic bond cleavage reaction in the model nucleoside forms of guanine and its major oxidation product, 8-oxoguanine. Base excision facilitated by four different nucleophiles (hydroxyl anion (fully activated water), formate-water complex (partially activated water), lysine, and proline) was considered, which spans nucleophiles involved in a collection of spontaneous and enzyme-catalyzed processes. Because some enzymes that catalyze deglycosylation can accommodate more than one orientation of the base with respect to the sugar moiety, the effects of the (anti/syn) base orientation on the barrier height were also considered. We find that the nucleophile has a very large effect on the overall (gas-phase) reaction energetics. Although this effect decreases in different (polar) environments, the nucleophile has the greatest influence on the overall reaction as compared to whether the base is damaged or to the base orientation. Furthermore, the effects are significant in environments that most closely resemble (nonpolar) enzymatic active sites. Our results provide a greater understanding of the relative effects of the nucleophile, damage to the nucleobase, and the nucleobase orientation with respect to the sugar moiety on the deglycosylation pathway, which provide qualitative explanations for relative base excision rates observed in some biological systems.
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Affiliation(s)
- Eun Jung Shim
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta T1K 3M4, Canada
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15
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Millen AL, Manderville RA, Wetmore SD. Conformational Flexibility of C8-Phenoxyl-2′-deoxyguanosine Nucleotide Adducts. J Phys Chem B 2010; 114:4373-82. [DOI: 10.1021/jp911993f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Andrea L. Millen
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Richard A. Manderville
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Stacey D. Wetmore
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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Vongsutilers V, Daft JR, Shaughnessy KH, Gannett PM. A general synthesis of C8-arylpurine phosphoramidites. Molecules 2009; 14:3339-52. [PMID: 19783928 PMCID: PMC6255102 DOI: 10.3390/molecules14093339] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Revised: 08/20/2009] [Accepted: 08/27/2009] [Indexed: 11/16/2022] Open
Abstract
A general scheme for the synthesis of C8-arylpurine phosphoramidites has been developed. C8-Arylation of C8-bromo-2′-deoxyguanosine is the key step and has been achieved through the use of a Suzuki coupling. Since the coupling reaction is conducted under aqueous conditions, it is unnecessary to protect and then deprotect the hydroxyl groups, thus saving several steps and improving overall yields. Once the C8-arylgroup is introduced, the glycosidic bond becomes very sensitive to acid catalyzed cleavage. Protection of the amino groups as the corresponding N,N-dimethylformamidine derivative improves stability of the derivatives. Synthetic C8-arylpurines were successfully used to prepare synthetic oligonucleotides.
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Affiliation(s)
- Vorasit Vongsutilers
- West Virginia University, Department of Basic Pharmaceutical Sciences, P.O. Box 9530, Morgantown, WV 26506, USA; E-mails: (V.V.); (J.R.D.)
| | - Jonathan R. Daft
- West Virginia University, Department of Basic Pharmaceutical Sciences, P.O. Box 9530, Morgantown, WV 26506, USA; E-mails: (V.V.); (J.R.D.)
| | - Kevin H. Shaughnessy
- Department of Chemistry and Center for Green Manufacturing, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, USA; E-mail: (K.H.S.)
| | - Peter M. Gannett
- West Virginia University, Department of Basic Pharmaceutical Sciences, P.O. Box 9530, Morgantown, WV 26506, USA; E-mails: (V.V.); (J.R.D.)
- Author to whom correspondence should be addressed; E-Mail:
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17
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Çeken B, Kízíl M. Synthesis and DNA-cleaving activity of a series of substituted arenediazonium ions. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2008; 34:546-57. [DOI: 10.1134/s1068162008040158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Millen AL, McLaughlin CK, Sun KM, Manderville RA, Wetmore SD. Computational and Experimental Evidence for the Structural Preference of Phenolic C-8 Purine Adducts. J Phys Chem A 2008; 112:3742-53. [DOI: 10.1021/jp712058a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea L. Millen
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and the Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Christopher K. McLaughlin
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and the Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Kewen M. Sun
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and the Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Richard A. Manderville
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and the Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Stacey D. Wetmore
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and the Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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Beda NV, Nedospasov AA. NO-dependent modifications of nucleic acids. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2007; 33:195-228. [PMID: 17476982 DOI: 10.1134/s106816200702001x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review is devoted to chemical transformations of nucleic acids and their components under the action of nitrogen oxide metabolites. The deamination reaction of bases is discussed in the context of possible competing transformations of its intermediates (nitrosamines, diazonium cations, diazotates, triazenes, and diazoanhydrides) and mechanisms of crosslink formation with proteins and nucleic acids. The oxidation and nitration of bases by NO2 is considered together with the possibility of radical transfer to domains from the base stacks in DNA. Reduction of redox potentials of bases as a result of stacking interactions explains the possibility of their reactions within nucleic acids with the oxidants whose redox potential is insufficient for the effective reactions with mononucleotides. Modifications of nucleic acids with peroxynitrite derivatives are discussed in the context of the effect of the DNA primary structure and the modification products formed on the reactivity of single bases. The possibility of reduction of nitro groups within modified bases to amino derivatives and their subsequent diazotation is considered. The substitution of oxoguanine for nitroguanine residues may result; the reductive diazotation can lead to undamaged guanine. The intermediate modified bases, e.g., 8-aminoguanine and 8-diazoguanine, were shown to participate in noncanonical base pairing, including the formation of more stable bonds with two bases, which is characteristic of the DNA Z-form. A higher sensitivity of RNA in comparison with DNA to NO-dependent modifications (NODMs) is predicted on the basis of the contribution of medium microheterogeneity and the known mechanisms of nitrosylation and nitration. The possible biological consequences of nucleic acids NODMs are briefly considered. It is shown that the NODMs under the action of nitrogen oxide metabolites generated by macrophages and similar cells in inflammations or infections should lead to a sharp increase in the number of mutations in the case of RNA-containing viruses. As a result, the defense mechanisms of the host organism may contribute to the appearance of new, including more dangerous, variants of infecting viruses.
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Western EC, Daft JR, Johnson EM, Gannett PM, Shaughnessy KH. Efficient one-step Suzuki arylation of unprotected halonucleosides, using water-soluble palladium catalysts. J Org Chem 2003; 68:6767-74. [PMID: 12919046 DOI: 10.1021/jo034289p] [Citation(s) in RCA: 179] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Modification of nucleosides to give pharmaceutically active compounds, mutagenesis models, and oligonucleotide structural probes continues to be of great interest. The aqueous-phase modification of unprotected halonucleosides is reported herein. Using a catalyst derived from tris(3-sulfonatophenyl)phosphine (TPPTS) and palladium acetate, 8-bromo-2'-deoxyguanosine (8-BrdG) is coupled with arylboronic acids to give 8-aryl-2'-deoxyguanosine adducts (8-ArdG) in excellent yield in a 2:1 water:acetonitrile solvent mixture. The TPPTS ligand was found to be superior to water-soluble alkylphosphines for this coupling reaction. The coupling chemistry has been extended to 8-bromo-2'-deoxyadenosine (8-BrdA) and 5-iodo-2'-deoxyuridine (5-IdU), as well as the ribonucleosides 8-bromoguanosine and 8-bromoadenosine. Good to excellent yields of arylated adducts are obtained in all cases. With use of tri(4,6-dimethyl-3-sulfonatophenyl)phosphine (TXPTS), the Suzuki coupling of 8-BrdA and 5-IdU can be accomplished in less than 1 h at room temperature. This methodology represents an efficient and general method for halonucleoside arylation that does not require prior protection of the nucleoside.
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Affiliation(s)
- Elizabeth C Western
- Department of Chemistry and the Center for Green Manufacturing, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, USA
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Quintero B, Cabeza MC, Martínez MI, Gutiérrez P, Martínez PJ. Dediazoniation of p-hydroxy and p-nitrobenzenediazonium ions in an aqueous medium: Interference by the chelating agent diethylenetriaminepentaacetic acid. CAN J CHEM 2003. [DOI: 10.1139/v03-088] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have made a comparative study of the dediazoniation of p-hydroxy and p-nitrobenzenediazonium ions. The electron-withdrawing and donating properties of the -NO2 and -OH groups strongly determine the reactivity of both compounds, thus exerting different influences upon the dediazoniation reaction. We describe here how the decomposition of p-hydroxy and p-nitrobenzenediazonium ions in a neutral aqueous medium follows a different pattern in the presence of the metal-chelator diethylenetriaminepentaacetic acid (DTPA). The decomposition rate of p-hydroxybenzene diazonium decreases whilst the decomposition of the p-nitrobenzenediazonium ion is enhanced. The experimental data are discussed with reference to a common scheme of interference for both benzenediazonium ions in the light of the radical-scavenging capacity of DTPA.Key words: p-hydroxybenzenediazonium ion, p-nitrobenzenediazonium ion, di-ethylenetriaminepentaacetic acid, dediazoniation, radical scavenging, artifacts.
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Gasparutto D, Dhérin C, Boiteux S, Cadet J. Excision of 8-methylguanine site-specifically incorporated into oligonucleotide substrates by the AlkA protein of Escherichia coli. DNA Repair (Amst) 2002; 1:437-47. [PMID: 12509232 DOI: 10.1016/s1568-7864(02)00016-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
8-Methyl-2'-deoxyguanosine (8-medGuo) has been shown to be a major stable alkylation product of 2'-deoxyguanosine induced by methyl radical attack on DNA. Moreover, by using primer extension assays, the latter DNA modification has recently been reported to be a miscoding lesion by generating G to C and G to T transversions and deletions in vitro. However, no data have been reported up to now, concerning the processing of this C8-alkylated nucleoside by the DNA repair machinery. Therefore, we have investigated the capability of excision of 8-methylguanine (8-meGua) site specifically incorporated into oligonucleotide substrates by several bacterial, yeast and mammalian DNA N-glycosylases. The results show that the 3-methyladenine (3-meAde) DNA glycosylase II (AlkA protein) from Escherichia coli is the only DNA N-glycosylase tested able to remove 8-meGua from double-stranded DNA fragments. Moreover, the activity of AlkA for 8-meGua varied markedly depending on the opposite base in DNA, being the highest with Adenine and Thymine and the lowest with Cytosine and Guanine. The removal of 8-meGua by AlkA protein was compared to that of 7-methylguanine (7-meGua) and hypoxanthine (Hx). The rank of damage as a substrate for AlkA being 7-meGua>8-meGua>Hx. In contrast, the human 3-meAde DNA N-glycosylase (Mpg) is not able to release 8-meGua paired with any of the four DNA bases. We also show that, DNA N-glycosylases involved in the removal of oxidative damage, such as Fpg or Nth proteins from E. coli, Ntg1, Ntg2 or Ogg1 proteins of Saccharomyces cerevisiae, or human Ogg1 do not release 8-meGua placed opposite any of the four DNA bases. Furthermore, HeLa and Chinese hamster ovary (CHO) cell free protein extracts do not show any cleavage activity at 8-meGua paired with adenine or cytosine, which suggests the absence of base excision repair (BER) of this lesion in mammalian cells.
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Affiliation(s)
- Didier Gasparutto
- Laboratoire des Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, UMR 5046 CEA-CNRS-UJF, Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 17 Avenue des Martyrs F-38054 Cedex 9, Grenoble, France
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Quintero B, Morales JJ, Quirós M, Martínez-Puentedura MI, Cabeza MC. Dediazoniation of p-hydroxybenzenediazonium ion in a neutral aqueous medium. Free Radic Biol Med 2000; 29:464-79. [PMID: 11020668 DOI: 10.1016/s0891-5849(00)00321-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The dediazoniation of p-hydroxybenzenediazonium ion (PDQ) in a neutral aqueous medium has been studied under controlled experimental conditions to prevent photochemical and/or heterolytic side-reactions. Oxygen increased the dediazoniation rate of PDQ and caused the appearance of quinone and hydroquinone. An accumulation of quinone deriving from the reduction of PDQ by hydroquinone was also observed. In ESR analyses with different spin traps, the most stable signal was identified as belonging to the adduct of the p-hydroxyphenyl radical, even in the presence of dimethylsulfoxide or ethanol. A general scheme is proposed including three pathways for the homolytic dediazoniation of PDQ. Pathway 1 represents dediazoniation induced by a hydroxyl ion, a slow process at neutral pH and an even slower one with deaerated samples; a favored quinoid structure is put forward to explain these results. In pathway 2, the formation of a semiquinone radical via the reaction of an aryl radical with oxygen is put forward to justify the increase in the dediazoniation rate in the presence of oxygen. In pathway 3, hydroquinone, produced by semiquinone dismutation, may act as a reducing agent.
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Affiliation(s)
- B Quintero
- Department of Physical Chemistry, University of Granada, Granada, Spain.
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Hix S, Augusto O. DNA methylation by tert-butyl hydroperoxide-iron (II): a role for the transition metal ion in the production of DNA base adducts. Chem Biol Interact 1999; 118:141-9. [PMID: 10359458 DOI: 10.1016/s0009-2797(99)00079-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Metabolic degradation of both endogenous and exogenous peroxides is associated with the etiology of several diseases including cancer. Tert-butyl hydroperoxide (TBHP) has been widely employed as a model compound to study the cytotoxicity and promoting effects of organic peroxides. Recently, we reported that incubations of TBHP with iron (II) and calf thymus DNA led to generation of high yields of methyl radicals and to DNA methylation. Interestingly, DNA was methylated to products expected from both free radical and ionic mechanisms such as 8-methylguanine (C8-MeGua) and 7-methylguanine (N7-MeGua), respectively. To elucidate the mechanisms by which methyl radicals can produce different types of DNA adducts, we examined the effects of transition metal ions (iron (II), iron (III) and copper (I)) and metal ion chelators (ethylenediamine-N,N,N",N"-tetraacetate (EDTA) and desferal) on the nature and the yields of the DNA adducts produced during TBHP decomposition. The results led us to propose that a direct methyl radical attack on DNA guanine residues produces C8-MeGua whereas N7-MeGua and 3-methyladenine (N3-MeAde) are likely to be produced by attack of nucleophilic DNA centers on methyl radical generated in situ by the assistance of transition metal ions bound to DNA.
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Affiliation(s)
- S Hix
- Departamento de Bioquímìca, Instituto de Química, Universidade de São Paulo, SP, Brazil
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Gannett PM, Powell JH, Rao R, Shi X, Lawson T, Kolar C, Toth B. C8-Arylguanine and C8-aryladenine formation in calf thymus DNA from arenediazonium ions. Chem Res Toxicol 1999; 12:297-304. [PMID: 10077493 DOI: 10.1021/tx980179f] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Arylhydrazides, arylhydrazines, and N-alkyl-N-arylnitrosamines are metabolized to arenediazonium ions which yield C8-arylpurine adducts in calf thymus and cellular DNA. The mechanism of adduct formation has not been fully elucidated. C8-Arylguanine adducts likely form from direct aryl radical (Ar*) addition to the C8 position of guanine. However, the amounts of C8-aryladenine adducts measured here are inconsistent with direct radical attack at the C8 position of adenine. An intermediate product, an aryltriazene, is likely formed which then decomposes to the C8-aryladenine adduct. We have demonstrated that N1-aryl-N3-purinyltriazene adducts are formed from a variety of para-substituted arenediazonium ions with adenine. Decomposition of the N1-aryl-N3-purinyltriazene, at high pH and elevated temperatures, has been shown to give C8-aryladenine derivatives, and a free radical mechanism for this process has been proposed. Here we show that this process can occur under physiological conditions and that the C8-aryladenine adduct can be quantitated by HPLC. ESR studies, in which DMPO was used as a spin trap, have been used to demonstrate the intermediacy of aryl radicals during the decomposition of the N1-aryl-N3-purinyltriazenes and to demonstrate that this process also occurs in calf thymus (ct) DNA treated with arenediazonium ions. These results suggest the involvement of an aryl radical in the formation of the observed DNA adducts. Finally, we have found that the treatment of ct DNA with arenediazonium ions produces a significant amount of depurination. Both the formation of C8-arylguanine and C8-aryladenine adducts and the generation of apurinic sites may contribute to the genotoxicity of arylhydrazides, arylhydrazines, N-alkyl-N-arylnitrosamines, and arenediazonium ions.
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Affiliation(s)
- P M Gannett
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, West Virginia University, P.O. Box 9530, Morgantown, West Virginia 26506, USA.
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Kwee JK, Armelin MS, Stefani HA, Augusto O. Cell proliferation induced by 8-oxoguanosine and 8-methylguanosine, two adducts produced by free radical attack on ribonucleosides and RNA. Chem Biol Interact 1998; 116:61-77. [PMID: 9877201 DOI: 10.1016/s0009-2797(98)00079-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ability of C8-substituted guanine (Gua) ribonucleosides to induce B cell proliferation has been well documented in the literature. These compounds are analogues of adducts formed from free radical attack on ribonucleosides and RNA. Here we examined the proliferative properties of two of these radical adducts, 8-methylguanosine (8-MeG) and 8-oxo-7,8-dihydroguanosine (8-OxoG) and compared them with those of the well studied B cell mitogen, 8-bromoguanosine (8-BrG). 8-MeG and 8-OxoG were synthesized in the considerable yields of 28, and 55%, respectively, and were characterized by UV, NMR and CG-MS. Their effects upon [3H]thymidine uptake into DNA by Swiss mouse splenocytes, mouse embryo 3T3 fibroblasts (A31) and mouse B16F10 melanoma were examined. Both guanosine (G) radical adducts were shown to increase [3H]thymidine uptake by mouse splenocytes but displayed selectivity in respect to continuous cell lines. 8-MeG acted upon 3T3 fibroblasts whereas 8-OxoG acted upon B16F10 melanoma. The non-physiological analogue 8-BrG acted upon all tested cells. Parallel experiments of cell counting, cytotoxicity,and cell sorting indicated that DNA synthesis induced by the C8-substituted G's reflected cell growth. It is proposed that the compounds act intracellularly because their proliferative effects were blocked in the presence of a nucleoside transport inhibitor but were not inhibited by an antagonist of the A2 purine receptor. The present results, taken together with data from the literature, suggest that in the case of 3T3 fibroblasts and mouse splenocytes the proliferative effects of the compounds are not dependent on metabolism through purine salvage pathways. In the case of melanoma, however, the compounds are likely to become part of the purine nucleoside pool. The demonstration that adducts produced by free radical attack on ribonucleosides and RNA are able to induce cell proliferation opens new perspectives for the understanding of free radical mediated carcinogenesis.
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Affiliation(s)
- J K Kwee
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
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