1
|
Reyes Y, Adhikary A, Wnuk SF. Nitrogen-Centered Radicals Derived from Azidonucleosides. Molecules 2024; 29:2310. [PMID: 38792171 PMCID: PMC11124349 DOI: 10.3390/molecules29102310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Azido-modified nucleosides have been extensively explored as substrates for click chemistry and the metabolic labeling of DNA and RNA. These compounds are also of interest as precursors for further synthetic elaboration and as therapeutic agents. This review discusses the chemistry of azidonucleosides related to the generation of nitrogen-centered radicals (NCRs) from the azido groups that are selectively inserted into the nucleoside frame along with the subsequent chemistry and biological implications of NCRs. For instance, the critical role of the sulfinylimine radical generated during inhibition of ribonucleotide reductases by 2'-azido-2'-deoxy pyrimidine nucleotides as well as the NCRs generated from azidonucleosides by radiation-produced (prehydrated and aqueous) electrons are discussed. Regio and stereoselectivity of incorporation of an azido group ("radical arm") into the frame of nucleoside and selective generation of NCRs under reductive conditions, which often produce the same radical species that are observed upon ionization events due to radiation and/or other oxidative conditions that are emphasized. NCRs generated from nucleoside-modified precursors other than azidonucleosides are also discussed but only with the direct relation to the same/similar NCRs derived from azidonucleosides.
Collapse
Affiliation(s)
- Yahaira Reyes
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA;
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA;
| | - Stanislaw F. Wnuk
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA;
| |
Collapse
|
2
|
Adjei D, Reyes Y, Kumar A, Ward S, Denisov SA, Alahmadi M, Sevilla MD, Wnuk SF, Mostafavi M, Adhikary A. Pathways of the Dissociative Electron Attachment Observed in 5- and 6-Azidomethyluracil Nucleosides: Nitrogen (N 2) Elimination vs Azide Anion (N 3-) Elimination. J Phys Chem B 2023; 127:1563-1571. [PMID: 36780335 PMCID: PMC9984991 DOI: 10.1021/acs.jpcb.2c08257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
5-Azidomethyl-2'-deoxyuridine (5-AmdU, 1) has been successfully employed for the metabolic labeling of DNA and fluorescent imaging of live cells. 5-AmdU also demonstrated significant radiosensitization in breast cancer cells via site-specific nitrogen-centered radical (π-aminyl (U-5-CH2-NH•), 2, and σ-iminyl (U-5-CH═N•), 3) formation. This work shows that these nitrogen-centered radicals are not formed via the reduction of the azido group in 6-azidomethyluridine (6-AmU, 4). Radical assignments were performed using electron spin resonance (ESR) in supercooled solutions, pulse radiolysis in aqueous solutions, and theoretical (DFT) calculations. Radiation-produced electron addition to 4 leads to the facile N3- loss, forming a stable neutral C-centered allylic radical (U-6-CH2•, 5) through dissociative electron attachment (DEA) via the transient negative ion, TNI (U-6-CH2-N3•-), in agreement with DFT calculations. In contrast, TNI (U-5-CH2-N3•-) of 1, via facile N2 loss (DEA) and protonation from the surrounding water, forms radical 2. Subsequently, 2 undergoes rapid H-atom abstraction from 1 and produces the metastable intermediate α-azidoalkyl radical (U-5-CH•-N3). U-5-CH•-N3 converts facilely to radical 3. N3- loss from U-6-CH2-N3•- is thermodynamically controlled, whereas N2 loss from U-5-CH2-N3•- is dictated by protonation from the surrounding waters and resonance conjugation of the azidomethyl side chain at C5 with the pyrimidine ring.
Collapse
Affiliation(s)
- Daniel Adjei
- Institut de Chimie Physique, UMR 8000 CNRS, Bât. 349, Université Paris-Saclay; 91405, Orsay, Cedex, France
| | - Yahaira Reyes
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, USA
| | - Anil Kumar
- Department of Chemistry, 146 Library Drive, Oakland University, Rochester, Michigan 48309, USA
| | - Samuel Ward
- Department of Chemistry, 146 Library Drive, Oakland University, Rochester, Michigan 48309, USA
| | - Sergey A. Denisov
- Institut de Chimie Physique, UMR 8000 CNRS, Bât. 349, Université Paris-Saclay; 91405, Orsay, Cedex, France
| | - Moaadh Alahmadi
- Department of Chemistry, 146 Library Drive, Oakland University, Rochester, Michigan 48309, USA
| | - Michael D. Sevilla
- Department of Chemistry, 146 Library Drive, Oakland University, Rochester, Michigan 48309, USA
| | - Stanislaw F. Wnuk
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, USA
| | - Mehran Mostafavi
- Institut de Chimie Physique, UMR 8000 CNRS, Bât. 349, Université Paris-Saclay; 91405, Orsay, Cedex, France
| | - Amitava Adhikary
- Department of Chemistry, 146 Library Drive, Oakland University, Rochester, Michigan 48309, USA
| |
Collapse
|
3
|
Mudgal M, Dang TP, Sobczak AJ, Lumpuy DA, Dutta P, Ward S, Ward K, Alahmadi M, Kumar A, Sevilla MD, Wnuk SF, Adhikary A. Site of Azido Substitution in the Sugar Moiety of Azidopyrimidine Nucleosides Influences the Reactivity of Aminyl Radicals Formed by Dissociative Electron Attachment. J Phys Chem B 2020; 124:11357-11370. [PMID: 33270461 DOI: 10.1021/acs.jpcb.0c08201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this work, electron-induced site-specific formation of neutral π-type aminyl radicals (RNH·) and their reactions with pyrimidine nucleoside analogs azidolabeled at various positions in the sugar moiety, e.g., at 2'-, 3'-, 4'-, and 5'- sites along with a model compound 3-azido-1-propanol (3AZPrOH), were investigated. Electron paramagnetic resonance (EPR) studies confirmed the site and mechanism of RNH· formation via dissociative electron attachment-mediated loss of N2 and subsequent facile protonation from the solvent employing the 15N-labeled azido group, deuterations at specific sites in the sugar and base, and changing the solvent from H2O to D2O. Reactions of RNH· were investigated employing EPR by warming these samples from 77 K to ca. 170 K. RNH· at a primary carbon site (5'-azido-2',5'-dideoxyuridine, 3AZPrOH) facilely converted to a σ-type iminyl radical (R═N·) via a bimolecular H-atom abstraction forming an α-azidoalkyl radical. RNH· when at a secondary carbon site (e.g., 2'-azido-2'-deoxyuridine) underwent bimolecular electrophilic addition to the C5═C6 double bond of a proximate pyrimidine base. Finally, RNH· at tertiary alkyl carbon (4'-azidocytidine) underwent little reaction. These results show the influence of the stereochemical and electronic environment on RNH· reactivity and allow the selection of those azidonucleosides that would be most effective in augmenting cellular radiation damage.
Collapse
Affiliation(s)
- Mukesh Mudgal
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Thao P Dang
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Adam J Sobczak
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Daniel A Lumpuy
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Priya Dutta
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Samuel Ward
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Katherine Ward
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Moaadh Alahmadi
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Anil Kumar
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Michael D Sevilla
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Stanislaw F Wnuk
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| |
Collapse
|
4
|
Kumar A, Becker D, Adhikary A, Sevilla MD. Reaction of Electrons with DNA: Radiation Damage to Radiosensitization. Int J Mol Sci 2019; 20:E3998. [PMID: 31426385 PMCID: PMC6720166 DOI: 10.3390/ijms20163998] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/01/2019] [Accepted: 08/12/2019] [Indexed: 01/19/2023] Open
Abstract
This review article provides a concise overview of electron involvement in DNA radiation damage. The review begins with the various states of radiation-produced electrons: Secondary electrons (SE), low energy electrons (LEE), electrons at near zero kinetic energy in water (quasi-free electrons, (e-qf)) electrons in the process of solvation in water (presolvated electrons, e-pre), and fully solvated electrons (e-aq). A current summary of the structure of e-aq, and its reactions with DNA-model systems is presented. Theoretical works on reduction potentials of DNA-bases were found to be in agreement with experiments. This review points out the proposed role of LEE-induced frank DNA-strand breaks in ion-beam irradiated DNA. The final section presents radiation-produced electron-mediated site-specific formation of oxidative neutral aminyl radicals from azidonucleosides and the evidence of radiosensitization provided by these aminyl radicals in azidonucleoside-incorporated breast cancer cells.
Collapse
Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - David Becker
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - Michael D Sevilla
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA.
| |
Collapse
|
5
|
Wen Z, Peng J, Tuttle PR, Ren Y, Garcia C, Debnath D, Rishi S, Hanson C, Ward S, Kumar A, Liu Y, Zhao W, Glazer PM, Liu Y, Sevilla MD, Adhikary A, Wnuk SF. Electron-Mediated Aminyl and Iminyl Radicals from C5 Azido-Modified Pyrimidine Nucleosides Augment Radiation Damage to Cancer Cells. Org Lett 2018; 20:7400-7404. [PMID: 30457873 PMCID: PMC6465127 DOI: 10.1021/acs.orglett.8b03035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Two classes of azido-modified pyrimidine nucleosides were synthesized as potential radiosensitizers; one class is 5-azidomethyl-2'-deoxyuridine (AmdU) and cytidine (AmdC), while the second class is 5-(1-azidovinyl)-2'-deoxyuridine (AvdU) and cytidine (AvdC). The addition of radiation-produced electrons to C5-azido nucleosides leads to the formation of π-aminyl radicals followed by facile conversion to σ-iminyl radicals either via a bimolecular reaction involving intermediate α-azidoalkyl radicals in AmdU/AmdC or by tautomerization in AvdU/AvdC. AmdU demonstrates effective radiosensitization in EMT6 tumor cells.
Collapse
Affiliation(s)
- Zhiwei Wen
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Jufang Peng
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Paloma R. Tuttle
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Yaou Ren
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Carol Garcia
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Dipra Debnath
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, United States
| | - Sunny Rishi
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, United States
| | - Cameron Hanson
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, United States
| | - Samuel Ward
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, United States
| | - Anil Kumar
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, United States
| | - Yanfeng Liu
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Weixi Zhao
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Peter M. Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Yuan Liu
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Michael D. Sevilla
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, United States
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, United States
| | - Stanislaw F. Wnuk
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| |
Collapse
|
6
|
Shelton J, Lu X, Hollenbaugh JA, Cho JH, Amblard F, Schinazi RF. Metabolism, Biochemical Actions, and Chemical Synthesis of Anticancer Nucleosides, Nucleotides, and Base Analogs. Chem Rev 2016; 116:14379-14455. [PMID: 27960273 DOI: 10.1021/acs.chemrev.6b00209] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleoside, nucleotide, and base analogs have been in the clinic for decades to treat both viral pathogens and neoplasms. More than 20% of patients on anticancer chemotherapy have been treated with one or more of these analogs. This review focuses on the chemical synthesis and biology of anticancer nucleoside, nucleotide, and base analogs that are FDA-approved and in clinical development since 2000. We highlight the cellular biology and clinical biology of analogs, drug resistance mechanisms, and compound specificity towards different cancer types. Furthermore, we explore analog syntheses as well as improved and scale-up syntheses. We conclude with a discussion on what might lie ahead for medicinal chemists, biologists, and physicians as they try to improve analog efficacy through prodrug strategies and drug combinations.
Collapse
Affiliation(s)
- Jadd Shelton
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , 1760 Haygood Drive, NE, Atlanta, Georgia 30322, United States
| | - Xiao Lu
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , 1760 Haygood Drive, NE, Atlanta, Georgia 30322, United States
| | - Joseph A Hollenbaugh
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , 1760 Haygood Drive, NE, Atlanta, Georgia 30322, United States
| | - Jong Hyun Cho
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , 1760 Haygood Drive, NE, Atlanta, Georgia 30322, United States
| | - Franck Amblard
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , 1760 Haygood Drive, NE, Atlanta, Georgia 30322, United States
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine , 1760 Haygood Drive, NE, Atlanta, Georgia 30322, United States
| |
Collapse
|
7
|
Kruman II, Henderson GI, Bergeson SE. DNA damage and neurotoxicity of chronic alcohol abuse. Exp Biol Med (Maywood) 2012; 237:740-7. [PMID: 22829701 DOI: 10.1258/ebm.2012.011421] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Chronic alcohol abuse results in a variety of pathological effects including damage to the brain. The causes of alcohol-induced brain pathology are presently unclear. Several mechanisms of pathogenicity of chronic alcoholism have been proposed, including accumulation of DNA damage in the absence of repair, resulting in genomic instability and death of neurons. Genomic instability is a unified genetic mechanism leading to a variety of neurodegenerative disorders. Ethanol also likely interacts with various metabolic pathways, including one-carbon metabolism (OCM). OCM is critical for the synthesis of DNA precursors, essential for DNA repair, and as a methyl donor for various methylation events, including DNA methylation. Both DNA repair and DNA methylation are critical for maintaining genomic stability. In this review, we outline the role of DNA damage and DNA repair dysfunction in chronic alcohol-induced neurodegeneration.
Collapse
Affiliation(s)
- Inna I Kruman
- Department of Pharmacology and Neuroscience, South Plains Alcohol and Addiction Research Center, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA.
| | | | | |
Collapse
|
8
|
Adhikary A, Khanduri D, Pottiboyina V, Rice CT, Sevilla MD. Formation of aminyl radicals on electron attachment to AZT: abstraction from the sugar phosphate backbone versus one-electron oxidation of guanine. J Phys Chem B 2010; 114:9289-99. [PMID: 20575557 DOI: 10.1021/jp103403p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Employing electron spin resonance (ESR) spectroscopy, we have characterized the radicals formed in 3'-azido-3'-deoxythymidine (3'-AZT) and in its 5'-analog 5'-azido-5'-deoxythymidine (5'-AZT) after electron attachment in gamma-irradiated aqueous (H(2)O or D(2)O) glassy (7.5 M LiCl) systems. ESR spectral studies and theoretical calculations show that the predominant site of electron capture in 3'-AZT and in 5'-AZT is at the azide group and not at the thymine moiety. The azide group in AZT is therefore more electron affinic than the most electron affinic DNA base, thymine. Electron attachment to 3'-AZT and 5'-AZT results in an unstable azide anion radical intermediate (RN(3)*(-)) that is too short-lived to be observed in our work even at 77 K. At 77 K, we observe the neutral aminyl radical (RNH*) after loss of N(2) from RN(3)*(-) followed by protonation of nitrene anion radical (RN*(-)) to give RNH*. The expected RN*(-) intermediate is not observed as protonation from water is complete at 77 K even under highly basic conditions. Formation of RND* in D(2)O solutions confirms water as the source of the NH proton in the RNH*. Our assignments to these radicals are aided by DFT calculations for hyperfine coupling constants that closely match the experimental values. On annealing to higher temperatures (ca. 160-170 K), RNH* undergoes bimolecular hydrogen abstraction reactions from the thymine methyl group and the sugar moiety resulting in the formation of the thymine allyl radical (UCH(2)*) and two sugar radicals, C3'* and C5'*. RNH* also results in one-electron oxidation of the guanine base in 3'-AZG. This work provides a potential mechanism for the reported radiosensitization effects of AZT.
Collapse
Affiliation(s)
- Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
| | | | | | | | | |
Collapse
|
9
|
van Bree C, Rodermond H, Leen R, Medema J, van Kuilenburg A. Cyclopentenyl cytosine increases gemcitabine radiosensitisation in human pancreatic cancer cells. Br J Cancer 2008; 98:1226-33. [PMID: 18349845 PMCID: PMC2359636 DOI: 10.1038/sj.bjc.6604287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The deoxycytidine analogue 2′,2′-difluoro-2′-deoxycytidine (dFdC, gemcitabine) is a potent radiosensitiser, but has limited efficacy in combination with radiotherapy in patients with pancreatic cancer due to acute toxicity. We investigated whether cyclopentenyl cytosine (CPEC), targetting the ‘de novo’ biosynthesis of cytidine triphosphate (CTP), could increase dFdC cytotoxicity alone or in combination with irradiation in a panel of human pancreatic cancer cells (Panc-1, Miapaca-2, BxPC-3). To investigate the role of deoxycytidine kinase (dCK), the rate-limiting enzyme in the activation of dFdC, human lung cancer cells without (dFdC-resistant SWg) and with an intact dCK gene (dFdC-sensitive SWp) were included. We found that CPEC (100–1000 nmol l−1) specifically reduced CTP levels in a dose-dependent manner that lasted up to 72 h in all cell lines. Preincubation with CPEC resulted in a dose-dependent increase in dFdC incorporated into the DNA only in dFdC-sensitive cells. Consequently, CPEC increased the effectiveness of dFdC (300 nmol l−1 for 4 h) only in dFdC-sensitive cells, which was accompanied by an increase in apoptosis. We also found that CPEC enhanced the radiosensitivity of cells treated with dFdC (30–300 nmol l−1 for 4 h). These results indicate that CPEC enhances the cytotoxicity of dFdC alone and in combination with irradiation in several human tumour cell lines with an intact dCK gene.
Collapse
Affiliation(s)
- C van Bree
- Department of Radiation Oncology, Academic Medical Centre-University of Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Centre for Experimental Molecular Medicine, Amsterdam, The Netherlands.
| | | | | | | | | |
Collapse
|