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Ferguson L, Madieh NS, Vaideanu A, Schatzlein A, Festa J, Singh H, Wells G, Bhakta S, Brucoli F. C2-linked alkynyl poly-ethylene glycol(PEG) adenosine conjugates as water-soluble adenosine receptor agonists. Chem Biol Drug Des 2023; 101:340-349. [PMID: 35993496 PMCID: PMC10087458 DOI: 10.1111/cbdd.14128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/09/2022] [Accepted: 07/30/2022] [Indexed: 01/14/2023]
Abstract
A series of 12 novel polyethylene-glycol(PEG)-alkynyl C2-adenosine(ADN) conjugates were synthesized using a robust Sonogashira coupling protocol and characterized by NMR spectroscopy and mass spectrometry analysis. The ADN-PEG conjugates showed null to moderate toxicity in murine macrophages and 12c was active against Mycobacterium aurum growth (MIC = 62.5 mg/L). The conjugates were not active against Mycobacterium bovis BCG. Conjugates 10b and 11b exhibited high water solubility with solubility values of 1.22 and 1.18 mg/ml, respectively, in phosphate buffer solutions at pH 6.8. Further, 10b and 11b induced a significant increase in cAMP accumulation in RAW264.7 cells comparable with that induced by adenosine. Analogues 10c, 11c and 12c were docked to the A1 , A2A , A2B and A3 adenosine receptors (ARs) using crystal-structures and homology models. ADN-PEG-conjugates bearing chains with up to five ethyleneoxy units could be well accommodated within the binding sites of A1 , A2A and A3 ARs. Docking studies showed that compound 10b and 11b were the best A2A receptor binders of the series, whereas 12c was the best binder for A1 AR. In summary, introduction of hydrophilic PEG substituents at the C2 of adenine ring significantly improved water solubility and did not affect AR binding properties of the ADN-PEG conjugates.
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Affiliation(s)
- Lindsay Ferguson
- School of Science, University of the West of Scotland, Paisley, UK
| | | | | | | | - Joseph Festa
- Leicester School of Allied Health Sciences, De Montfort University, Leicester, UK
| | - Harprit Singh
- Leicester School of Allied Health Sciences, De Montfort University, Leicester, UK
| | - Geoffrey Wells
- UCL School of Pharmacy, University College London, London, UK
| | - Sanjib Bhakta
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK
| | - Federico Brucoli
- Leicester School of Pharmacy, De Montfort University, Leicester, UK
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2
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Jung H, Rayala NK, Lee S. Effects of N7-Alkylguanine Conformation and Metal Cofactors on the Translesion Synthesis by Human DNA Polymerase η. Chem Res Toxicol 2022; 35:512-521. [PMID: 35239327 DOI: 10.1021/acs.chemrestox.1c00416] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Non-enzymatic alkylation on DNA often generates N7-alkyl-2'-deoxyguanosine (N7alkylG) adducts as major lesions. N7alkylG adducts significantly block replicative DNA polymerases and can be bypassed by translesion synthesis (TLS) polymerases such as polymerase η (polη). To gain insights into the bypass of N7alkylG by TLS polymerases, we conducted kinetic and structural studies of polη catalyzing across N7BnG, a genotoxic lesion generated by the carcinogenic N-nitrosobenzylmethylamine. The presence of templating N7BnG in the polη catalytic site decreased the replication fidelity by ∼9-fold, highlighting the promutagenicity of N7BnG. The catalytic efficiency for dCTP incorporation opposite N7BnG decreased ∼22-fold and ∼7-fold compared to the incorporation opposite undamaged guanine in the presence of Mg2+ and Mn2+, respectively. A crystal structure of the complexes grown with polη, templating N7BnG, incoming dCTP, and Mg2+ ions showed the lack of the incoming nucleotide and metal cofactors in the polη catalytic site. Interestingly, the templating N7BnG adopted a syn conformation, which has not been observed in the published N7alkylG structures. The preferential formation of syn-N7BnG conformation at the templating site may deter the binding of an incoming dCTP, causing the inefficient bypass by polη. In contrast, the use of Mn2+ in place of Mg2+ in co-crystallization yielded a ternary complex displaying an anti-N7BnG:dCTP base pair and catalytic metal ions, which would be a close mimic of a catalytically competent state. We conclude that certain bulky N7-alkylG lesions can slow TLS polymerase-mediated bypass by adopting a catalytically unfavorable syn conformation in the replicating base pair site.
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Affiliation(s)
- Hunmin Jung
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Naveen Kumar Rayala
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Seongmin Lee
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, USA
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3
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Xiao S, Lee W, Chen F, Zavalij PY, Gutierrez O, Davis JT. Oxidation of 8-thioguanosine gives redox-responsive hydrogels and reveals intermediates in a desulfurization pathway. Chem Commun (Camb) 2020; 56:6981-6984. [PMID: 32436517 DOI: 10.1039/d0cc02926b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A disulfide made by oxidation of 8-thioguanosine is a supergelator. The hydrogels are redox-responsive, as they disassemble upon either reduction or oxidation of the S-S bond. We also identified this disulfide, and 2 other compounds, as intermediates in oxidative desulfurization of 8-thioG to guanosine.
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Affiliation(s)
- Songjun Xiao
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742, USA.
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4
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Abstract
In nature and in the test tube, nucleic acids occur in many different forms. Apart from single-stranded, coiled molecules, DNA and RNA prefer to form helical arrangements, in which the bases are stacked to shield their hydrophobic surfaces and expose their polar edges. Focusing on double helices, we describe the crucial role played by symmetry in shaping DNA and RNA structure. The base pairs in nucleic-acid double helices display rotational pseudo-symmetry. In the Watson–Crick base pairs found in naturally occurring DNA and RNA duplexes, the symmetry axis lies in the base-pair plane, giving rise to two different helical grooves. In contrast, anti-Watson–Crick base pairs have a dyad axis perpendicular to the base-pair plane and identical grooves. In combination with the base-pair symmetry, the syn/anti conformation of paired nucleotides determines the parallel or antiparallel strand orientation of double helices. DNA and RNA duplexes in nature are exclusively antiparallel. Watson–Crick base-paired DNA or RNA helices display either right-handed or left-handed helical (pseudo-) symmetry. Genomic DNA is usually in the right-handed B-form, and RNA double helices adopt the right-handed A-conformation. Finally, there is a higher level of helical symmetry in superhelical DNA in which B-form double strands are intertwined in a right- or left-handed sense.
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5
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Martinez-Fernandez L, Gustavsson T, Diederichsen U, Improta R. Excited State Dynamics of 8-Vinyldeoxyguanosine In Aqueous Solution Studied by Time-Resolved Fluorescence Spectroscopy and Quantum Mechanical Calculations. Molecules 2020; 25:E824. [PMID: 32070032 PMCID: PMC7071107 DOI: 10.3390/molecules25040824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 02/08/2023] Open
Abstract
The fluorescent base guanine analog, 8-vinyl-deoxyguanosine (8vdG), is studied in solution using a combination of optical spectroscopies, notably femtosecond fluorescence upconversion and quantum chemical calculations, based on time-dependent density functional theory (TD-DFT) and including solvent effect by using a mixed discrete-continuum model. In all investigated solvents, the fluorescence is very long lived (3-4 ns), emanating from a stable excited state minimum with pronounced intramolecular charge-transfer character. The main non-radiative decay channel features a sizeable energy barrier and it is affected by the polarity and the H-bonding properties of the solvent. Calculations provide a picture of dynamical solvation effects fully consistent with the experimental results and show that the photophysical properties of 8vdG are modulated by the orientation of the vinyl group with respect to the purine ring, which in turn depends on the solvent. These findings may have importance for the understanding of the fluorescence properties of 8vdG when incorporated in a DNA helix.
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Affiliation(s)
- Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and IADCHEM (Institute for Advanced Research in Chemistry) Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain;
| | - Thomas Gustavsson
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
| | - Ulf Diederichsen
- Univ Goettingen, Inst Organ & Biomol Chem, Tammannstr 2, D-37077 Goettingen, Germany;
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
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6
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Bose S, Hodgson DRW. Stereoselective Syntheses of 3'-Hydroxyamino- and 3'-Methoxyamino-2',3'-Dideoxynucleosides. Org Lett 2019; 21:9084-9088. [PMID: 31668079 PMCID: PMC7007280 DOI: 10.1021/acs.orglett.9b03474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Aminonucleosides
are used as key motifs in medicinal and bioconjugate
chemistry; however, existing strategies toward 3′-hypernucleophilic
amine systems do not readily deliver deoxyribo-configured
products. We report diastereoselective syntheses of deoxyribo- and deoxyxylo-configured 3′-hydroxyamino-
and 3′-methoxyamino-nucelosides from 3′-imine intermediates.
The presence or absence of the 5′-hydroxyl-group protection
dictates facial selectivity via inter- or intramolecular delivery
of hydride from BH3 (borane). Protecting group screening
gave one access to previously unknown 3′-methoxyamino-deoxyguanosine
derivatives.
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Affiliation(s)
- Sritama Bose
- Durham University , Department of Chemistry , Lower Mountjoy, Stockton Road , Durham , DH1 3LE , United Kingdom
| | - David R W Hodgson
- Durham University , Department of Chemistry , Lower Mountjoy, Stockton Road , Durham , DH1 3LE , United Kingdom
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7
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Munte CE, Karl M, Kauter W, Eberlein L, Pham TV, Erlach MB, Kast SM, Kremer W, Kalbitzer HR. High pressure response of 1H NMR chemical shifts of purine nucleotides. Biophys Chem 2019; 254:106261. [PMID: 31522070 DOI: 10.1016/j.bpc.2019.106261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/01/2019] [Accepted: 09/01/2019] [Indexed: 11/25/2022]
Abstract
The study of the pressure response by NMR spectroscopy provides information on the thermodynamics of conformational equilibria in proteins and nucleic acids. For obtaining a database for expected pressure effects on free nucleotides and nucleotides bound in macromolecular complexes, the pressure response of 1H chemical shifts and J-coupling constants of the purine 5'-ribonucleotides AMP, ADP, ATP, GMP, GDP, and GTP were studied in the absence and presence of Mg2+-ions. Experiments are supported by quantum-chemical calculations of populations and chemical shift differences in order to corroborate structural interpretations and to estimate missing data for AMP. The preference of the ribose S puckering obtained from the analysis of the experimental J-couplings is also confirmed by the calculations. In addition, the pressure response of the non-hydrolysable GTP analogues GppNHp, GppCH2p, and GTPγS was examined within a pressure range up to 200 MPa. As observed earlier for 31P NMR chemical shifts of these nucleotides the pressure dependence of chemical shifts is clearly non-linear in most cases. In di- and tri-phospho nucleosides, the resonances of the two protons bound to the ribose 5' carbon are non-equivalent and can be observed separately. The gg-rotamer at C4'- C5' bond is strongly preferred and the downfield shifted resonance can be assigned to the H5″ proton in the nucleotides. In contrast, in adenosine itself the frequencies of the two resonances are interchanged.
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Affiliation(s)
- Claudia E Munte
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Matthias Karl
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Waldemar Kauter
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Lukas Eberlein
- TU Dortmund University, Physical Chemistry III, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Thuy-Vy Pham
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Markus Beck Erlach
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Stefan M Kast
- TU Dortmund University, Physical Chemistry III, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Werner Kremer
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Hans Robert Kalbitzer
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany.
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8
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Wang Y, Zhu Y, Hu Y, Zeng G, Zhang Y, Zhang C, Feng C. How to Construct DNA Hydrogels for Environmental Applications: Advanced Water Treatment and Environmental Analysis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1703305. [PMID: 29450972 DOI: 10.1002/smll.201703305] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 11/23/2017] [Indexed: 06/08/2023]
Abstract
With high binding affinity, porous structures, safety, green, programmability, etc., DNA hydrogels have gained increasing recognition in the environmental field, i.e., advanced treatment technology of water and analysis of specific pollutants. DNA hydrogels have been demonstrated as versatile potential adsorbents, immobilization carriers of bioactive molecules, catalysts, sensors, etc. Moreover, altering components or choosing appropriate functional DNA optimizes environment-oriented hydrogels. However, the lack of comprehensive information hinders the continued optimization. The principle used to fabricate the most suitable hydrogels in terms of the requirements is the focus of this Review. First, different fabrication strategies are introduced and the ideal characteristic for environmental applications is in focus. Subsequently, recent environmental applications and the development of diverse DNA hydrogels regarding their synthesis mechanism are summarized. Finally, the Review provides an insight into the remaining challenging and future perspectives in environmental applications.
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Affiliation(s)
- Yingrong Wang
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
| | - Yuan Zhu
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
| | - Yi Hu
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
| | - Yi Zhang
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Chang Zhang
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
| | - Chongling Feng
- Research Center of Environmental Science and Engineering, Center South University of Forestry and Technology, Shaoshan South Road, Changsha, 410004, China
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9
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Dracínský M, Pohl R. Determination of the Nucleic Acid Adducts Structure at the Nucleoside/Nucleotide Level by NMR Spectroscopy. Chem Res Toxicol 2016; 28:155-65. [PMID: 25584790 DOI: 10.1021/tx5004535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All living organisms are exposed to xenobiotics from the environment. The exposure can lead to the formation of covalent adducts of xenobiotics or their metabolites with nucleic acids (NAs).The knowledge of NA adduct structure provides valuable information n the mechanism of carcinogenesis on a molecular level. While NMR spectroscopy is extremely successful in structural analysis of many classes of molecules ranging from small inorganic and organic molecules to large biomacromolecules, the structural analysis of NA adducts by NMR spectroscopy is accompanied by some challenges. First, the structural diversity of the adducts is very large; the electrophilic species generated from the metabolism of xenobiotics can attack various atoms of the nucleobases, and new rings are frequently formed. The second challenge in the DNA adducts structure determination is the low sensitivity of NMR spectroscopy and low amount of the adducts isolated from in vivo experiments. Recent developments of NMR hardware and experimental methods have led, however, to unprecedented sensitivity. This contribution reviews NMR techniques that are commonly applied in the determination of nucleic acid adducts structure at the nucleoside/nucleotide level. These NMR techniques and the large structural heterogeneity of NA adducts are demonstrated on recent examples (mostly published after 2000) of NA adducts structure determined by NMR. Most of the examples report 2′-deoxyribonucles(t)ide derivatives, but RNA adducts are also briefly discussed. The influence of the formation of NA adducts on nucleoside conformation (particularly syn/anti orientation of the base) is also demonstrated on recent examples.
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10
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Abstract
This paper highlights recent developments in the design and construction of functional materials such as supramolecular hydrogels and ion channels using a guanine motif as a self-assembling building block.
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Affiliation(s)
- Jyotirmayee Dash
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India.
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11
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Abstract
A G4-quartet based hydrogel formed by self-assembly of borate esters of 5′-deoxy-5′-iodoguanosine (5′-IG 2) undergoes in situ cyclization to give 5′-deoxy-N3,5′-cycloguanosine (5′-cG 3). Formation of 5′-cG 3 causes self-destruction of the gel. This intramolecular cyclization can be used to release nucleoside analogs that have been pre-incorporated into the gel network.
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Affiliation(s)
- Taylor N. Plank
- Department of Chemistry & Biochemistry
- University of Maryland
- College Park
- USA
| | - Jeffery T. Davis
- Department of Chemistry & Biochemistry
- University of Maryland
- College Park
- USA
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12
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Pergolizzi G, Cominetti MMD, Butt JN, Field RA, Bowater RP, Wagner GK. Base-modified NAD and AMP derivatives and their activity against bacterial DNA ligases. Org Biomol Chem 2015; 13:6380-98. [PMID: 25974621 DOI: 10.1039/c5ob00294j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We report the chemical synthesis and conformational analysis of a collection of 2-, 6- and 8-substituted derivatives of β-NAD(+) and AMP, and their biochemical evaluation against NAD(+)-dependent DNA ligases from Escherichia coli and Mycobacterium tuberculosis. Bacterial DNA ligases are validated anti-microbial targets, and new strategies for their inhibition are therefore of considerable scientific and practical interest. Our study includes several pairs of β-NAD(+) and AMP derivatives with the same substitution pattern at the adenine base. This has enabled the first direct comparison of co-substrate and inhibitor behaviour against bacterial DNA ligases. Our results suggest that an additional substituent in position 6 or 8 of the adenine base in β-NAD(+) is detrimental for activity as either co-substrate or inhibitor. In contrast, substituents in position 2 are not only tolerated, but appear to give rise to a new mode of inhibition, which targets the conformational changes these DNA ligases undergo during catalysis. Using a molecular modelling approach, we highlight that these findings have important implications for our understanding of ligase mechanism and inhibition, and may provide a promising starting point for the rational design of a new class of inhibitors against NAD(+)-dependent DNA ligases.
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Affiliation(s)
- Giulia Pergolizzi
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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13
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Garate JA, Oostenbrink C. Free-energy differences between states with different conformational ensembles. J Comput Chem 2013; 34:1398-408. [PMID: 23526629 DOI: 10.1002/jcc.23276] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 02/20/2013] [Accepted: 02/23/2013] [Indexed: 11/10/2022]
Abstract
Multiple conformations separated by high-energy barriers represent a challenging problem in free-energy calculations due to the difficulties in achieving adequate sampling. We present an application of thermodynamic integration (TI) in conjunction with the local elevation umbrella sampling (LE/US) method to improve convergence in alchemical free-energy calculations. TI-LE/US was applied to the guanosine triphosphate (GTP) to 8-Br-GTP perturbation, molecules that present high-energy barriers between the anti and syn states and that have inverted preferences for those states. The convergence and reliability of TI-LE/US was assessed by comparing with previous results using the enhanced-sampling one-step perturbation (OSP) method. A linear interpolation of the end-state biasing potentials was sufficient to dramatically improve sampling along the chosen reaction coordinate. Conformational free-energy differences were also computed for the syn and anti states and compared to experimental and theoretical results. Additionally, a coupled OSP with LE/US was carried out, allowing the calculation of conformational and alchemical free energies of GTP and 8-substituted GTP analogs.
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Affiliation(s)
- Jose Antonio Garate
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
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Wei C, Pohorille A. Permeation of aldopentoses and nucleosides through fatty acid and phospholipid membranes: implications to the origins of life. ASTROBIOLOGY 2013; 13:177-188. [PMID: 23397957 DOI: 10.1089/ast.2012.0901] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Permeation of aldopentoses and nucleosides through fatty acid and phospholipid membranes was investigated by way of molecular dynamics simulations. Calculated permeability coefficients of membranes to aldopentoses, which exist predominantly in the pyranose form, are in a very good agreement with experimental results. The unexpected preferential permeation of ribose, compared to its diastereomers, found by Sacerdote and Szostak, is explained in terms of inter- and intramolecular interactions involving hydroxyl groups. In aqueous solution, these groups favor the formation of intermolecular hydrogen bonds with neighboring water molecules. Inside the membrane, however, they form intramolecular hydrogen bonds, which in ribose are arranged in a chain. In its diastereomers this chain is broken, which yields higher free energy barrier to transfer through membranes. Faster permeation of ribose would lead to its preferential accumulation inside cells if sugars were converted sufficiently quickly to nonpermeable derivatives. An estimate for the rate of such reaction was derived. Preferential accumulation of ribose would increase the probability of correct monomers' incorporation during synthesis of nucleic acids inside protocells. The same mechanism does not apply to nucleosides or their activated derivatives because sugars are locked in the furanose form, which contains fewer exocyclic hydroxyl groups than does pyranose. The results of this study underscore concerted early evolution of membranes and the biochemical processes that they encapsulated.
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Affiliation(s)
- Chenyu Wei
- NASA Ames Research Center, Moffett Field, California 94035, USA
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15
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Recent advances in cyclonucleosides: C-cyclonucleosides and spore photoproducts in damaged DNA. Molecules 2012; 17:11630-54. [PMID: 23023688 PMCID: PMC6268316 DOI: 10.3390/molecules171011630] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 09/25/2012] [Accepted: 09/26/2012] [Indexed: 12/04/2022] Open
Abstract
Cyclonucleosides which are fixed in a specific conformation around the glycosyl bond by a carbon and heteroatom chain constitute a unique category of nucleoside derivatives. Because they are structural analogs, cyclonucleosides and oligodeoxynucleotides containing them would be useful tools for investigating the biological functions and conformations of DNA, RNA as well as their steric interactions with proteins. C-Cyclonucleosides bridged by a carbon chain between the base and sugar moieties are the most attractive from the synthetic points of view as well as for use as biological tools. In this review, recent progress of the synthesis of C-cyclonucleosides is surveyed. Among the C-cyclonucleosides, 5′,8-C-cyclodeoxyadenosine is one of the well-known derivatives of which the first practical synthesis was reported over 30 years ago. Recently, 5′,8-C-cyclodeoxyadenosine has attracted considerable interest as a biomarker, since its formation in oxidatively-damaged DNA is considered to be related to various diseases and aging. Another important analogue of cyclonucleosides is a unique thymidine phosphate dimer, a so-called spore photoproduct, which has been found in photo-damaged DNA. Recent advances in the synthesis, mechanism-studies, and stereochemical preference of repairing enzymes related to 5′,8-C-cyclodeoxyadenosine and spore photoproducts are also reviewed.
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16
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Egea PF, Muller-Steffner H, Kuhn I, Cakir-Kiefer C, Oppenheimer NJ, Stroud RM, Kellenberger E, Schuber F. Insights into the mechanism of bovine CD38/NAD+glycohydrolase from the X-ray structures of its Michaelis complex and covalently-trapped intermediates. PLoS One 2012; 7:e34918. [PMID: 22529956 PMCID: PMC3329556 DOI: 10.1371/journal.pone.0034918] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 03/06/2012] [Indexed: 01/02/2023] Open
Abstract
Bovine CD38/NAD+glycohydrolase (bCD38) catalyses the hydrolysis of NAD+ into nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose (cADPR). We solved the crystal structures of the mono N-glycosylated forms of the ecto-domain of bCD38 or the catalytic residue mutant Glu218Gln in their apo state or bound to aFNAD or rFNAD, two 2′-fluorinated analogs of NAD+. Both compounds behave as mechanism-based inhibitors, allowing the trapping of a reaction intermediate covalently linked to Glu218. Compared to the non-covalent (Michaelis) complex, the ligands adopt a more folded conformation in the covalent complexes. Altogether these crystallographic snapshots along the reaction pathway reveal the drastic conformational rearrangements undergone by the ligand during catalysis with the repositioning of its adenine ring from a solvent-exposed position stacked against Trp168 to a more buried position stacked against Trp181. This adenine flipping between conserved tryptophans is a prerequisite for the proper positioning of the N1 of the adenine ring to perform the nucleophilic attack on the C1′ of the ribofuranoside ring ultimately yielding cADPR. In all structures, however, the adenine ring adopts the most thermodynamically favorable anti conformation, explaining why cyclization, which requires a syn conformation, remains a rare alternate event in the reactions catalyzed by bCD38 (cADPR represents only 1% of the reaction products). In the Michaelis complex, the substrate is bound in a constrained conformation; the enzyme uses this ground-state destabilization, in addition to a hydrophobic environment and desolvation of the nicotinamide-ribosyl bond, to destabilize the scissile bond leading to the formation of a ribooxocarbenium ion intermediate. The Glu218 side chain stabilizes this reaction intermediate and plays another important role during catalysis by polarizing the 2′-OH of the substrate NAD+. Based on our structural analysis and data on active site mutants, we propose a detailed analysis of the catalytic mechanism.
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Affiliation(s)
- Pascal F. Egea
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail: (PFE); (FS)
| | - Hélène Muller-Steffner
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Isabelle Kuhn
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Céline Cakir-Kiefer
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
- Unité de Recherche Animal et Fonctionnalités des Produits Animaux, UR AFPA, Nancy Université, Vandoeuvre-les-Nancy, France
| | - Norman J. Oppenheimer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Robert M. Stroud
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Esther Kellenberger
- Laboratoire d'Innovation Thérapeutique, UMR 7200 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
| | - Francis Schuber
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch, France
- * E-mail: (PFE); (FS)
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17
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Moreau C, Kirchberger T, Zhang B, Thomas MP, Weber K, Guse AH, Potter BVL. Aberrant cyclization affords a C-6 modified cyclic adenosine 5'-diphosphoribose analogue with biological activity in Jurkat T cells. J Med Chem 2012; 55:1478-89. [PMID: 22248391 PMCID: PMC3285147 DOI: 10.1021/jm201127y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two nicotinamide adenine dinucleotide (NAD(+)) analogues modified at the 6 position of the purine ring were synthesized, and their substrate properties toward Aplysia californica ADP-ribosyl cyclase were investigated. 6-N-Methyl NAD(+) (6-N-methyl nicotinamide adenosine 5'-dinucleotide 10) hydrolyzes to give the linear 6-N-methyl ADPR (adenosine 5'-diphosphoribose, 11), whereas 6-thio NHD(+) (nicotinamide 6-mercaptopurine 5'-dinucleotide, 17) generates a cyclic dinucleotide. Surprisingly, NMR correlation spectra confirm this compound to be the N1 cyclic product 6-thio N1-cIDPR (6-thio cyclic inosine 5'-diphosphoribose, 3), although the corresponding 6-oxo analogue is well-known to cyclize at N7. In Jurkat T cells, unlike the parent cyclic inosine 5'-diphosphoribose N1-cIDPR 2, 6-thio N1-cIDPR antagonizes both cADPR- and N1-cIDPR-induced Ca(2+) release but possesses weak agonist activity at higher concentration. 3 is thus identified as the first C-6 modified cADPR (cyclic adenosine 5'-diphosphoribose) analogue antagonist; it represents the first example of a fluorescent N1-cyclized cADPR analogue and is a new pharmacological tool for intervention in the cADPR pathway of cellular signaling.
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Affiliation(s)
- Christelle Moreau
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
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18
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19
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Buerkle LE, von Recum HA, Rowan SJ. Toward potential supramolecular tissue engineering scaffolds based on guanosine derivatives. Chem Sci 2012. [DOI: 10.1039/c1sc00729g] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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20
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Seio K, Kurohagi S, Kodama E, Masaki Y, Tsunoda H, Ohkubo A, Sekine M. Short-RNA selective binding of oligonucleotides modified using adenosine and guanosine derivatives that possess cyclohexyl phosphates as substituents. Org Biomol Chem 2011; 10:994-1006. [PMID: 22143376 DOI: 10.1039/c1ob06580g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed new artificial oligonucleotides which distinguish short RNA targets from long ones. The modification of the 5' termini of oligonucleotides by using adenosine derivatives that possess a bulky cyclohexyl phosphate moiety at their base moiety and a phosphate group at the position of their 5'-hydroxyl group maximized their short RNA selectivity. The 2'-O-methyl-RNA (5'-XC(m)A(m)A(m)C(m)C(m)U(m)A(m)C(m)U(m)) having these modifications exhibits ca. 10 °C higher T(m) in the duplexes with the complementary short RNA (3'-GUUGGAUGA-5') than with the long RNA (3'-AUUAUAUGUUGGAUGAUGGUUA-5'). The oligodeoxynucleotides having the same modification exhibited similar selectivity. Such short-RNA selective binding of terminally modified oligonucleotides can be employed to distinguish between mature microRNAs and pre-microRNAs.
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Affiliation(s)
- Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Japan.
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21
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Dumas A, Luedtke NW. Fluorescence properties of 8-(2-pyridyl)guanine "2PyG" as compared to 2-aminopurine in DNA. Chembiochem 2011; 12:2044-51. [PMID: 21786378 DOI: 10.1002/cbic.201100214] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Indexed: 12/24/2022]
Abstract
Because of their environment-sensitive fluorescence quantum yields, base analogues such as 2-aminopurine (2AP), 6-methylisoxanthopterin (6-MI), and 3-methylisoxanthopterin (3-MI) are widely used in nucleic-acid folding and catalysis assays. Emissions from these guanine mimics are quenched by base-stacking interactions and collisions with purine residues. Fluorescent base analogues that remain highly emissive in folded nucleic acids can provide sensitive means to differentiate DNA/RNA structures by participating in energy transfer from proximal ensembles of unmodified nucleobases. The development of new, highly emissive guanine mimics capable of proper base stacking and base-pairing interactions is an important prerequisite to this approach. Here we report a comparison of the most commonly used probe, 2-aminopurine (2AP), to 8-(2-pyridyl)-2'-deoxyguanosine (2PyG). The photophysical properties of these purine derivatives are very different. 2PyG exhibits enhanced fluorescence quantum yields upon its incorporation into folded nucleic acids--approximately 50-fold brighter fluorescence intensity than 2AP in the context of duplex DNA. Due to its bright fluorescence and compatibility with proper DNA folding, 2PyG can be used to accurately quantify energy-transfer efficiencies, whereas 2AP is much less sensitive to structure-specific trends in energy transfer. When using nucleoside monomers, Stern-Volmer plots of 2AP fluorescence revealed upward curvature of F(0) /F upon titration of guanosine monophoshate (GMP), whereas 2PyG exhibited unusual downward curvature of F(0) /F that resulted in a recovery of fluorescence at high GMP concentrations. These results are consistent with the trends observed for 2PyG- and 2AP-containing oligonucleotides, and furthermore suggest that solutions containing high concentrations of GMP can, in some ways, mimic the high local nucleobase densities of folded nucleic acids.
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Affiliation(s)
- Anaëlle Dumas
- Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, Zürich 8057, Switzerland
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22
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Moreau C, Ashamu GA, Bailey VC, Galione A, Guse AH, Potter BVL. Synthesis of cyclic adenosine 5'-diphosphate ribose analogues: a C2'endo/syn "southern" ribose conformation underlies activity at the sea urchin cADPR receptor. Org Biomol Chem 2011; 9:278-90. [PMID: 20976353 PMCID: PMC3172588 DOI: 10.1039/c0ob00396d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 09/14/2010] [Indexed: 12/03/2022]
Abstract
Novel 8-substituted base and sugar-modified analogues of the Ca(2+) mobilizing second messenger cyclic adenosine 5'-diphosphate ribose (cADPR) were synthesized using a chemoenzymatic approach and evaluated for activity in sea urchin egg homogenate (SUH) and in Jurkat T-lymphocytes; conformational analysis investigated by (1)H NMR spectroscopy revealed that a C2'endo/syn conformation of the "southern" ribose is crucial for agonist or antagonist activity at the SUH-, but not at the T cell-cADPR receptor.
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Affiliation(s)
- Christelle Moreau
- Wolfson Laboratory of Medicinal Chemistry , Department of Pharmacy and Pharmacology , University of Bath , Bath , UK BA2 7AY . ; Fax: +44 1225 386114 ; Tel: +44 1225 386639
| | - Gloria A. Ashamu
- Wolfson Laboratory of Medicinal Chemistry , Department of Pharmacy and Pharmacology , University of Bath , Bath , UK BA2 7AY . ; Fax: +44 1225 386114 ; Tel: +44 1225 386639
| | - Victoria C. Bailey
- Wolfson Laboratory of Medicinal Chemistry , Department of Pharmacy and Pharmacology , University of Bath , Bath , UK BA2 7AY . ; Fax: +44 1225 386114 ; Tel: +44 1225 386639
| | - Antony Galione
- Department of Pharmacology , University of Oxford , Mansfield Road , Oxford , UK OX1 3QT
| | - Andreas H. Guse
- Institute of Biochemistry and Molecular Biology I: Cellular Signal Transduction , University Medical Center Hamburg-Eppendorf , Germany
| | - Barry V. L. Potter
- Wolfson Laboratory of Medicinal Chemistry , Department of Pharmacy and Pharmacology , University of Bath , Bath , UK BA2 7AY . ; Fax: +44 1225 386114 ; Tel: +44 1225 386639
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23
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Petrelli R, Sham YY, Chen L, Felczak K, Bennett E, Wilson D, Aldrich C, Yu JS, Cappellacci L, Franchetti P, Grifantini M, Mazzola F, Di Stefano M, Magni G, Pankiewicz KW. Selective inhibition of nicotinamide adenine dinucleotide kinases by dinucleoside disulfide mimics of nicotinamide adenine dinucleotide analogues. Bioorg Med Chem 2009; 17:5656-64. [PMID: 19596199 DOI: 10.1016/j.bmc.2009.06.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 06/03/2009] [Accepted: 06/06/2009] [Indexed: 11/26/2022]
Abstract
Diadenosine disulfide (5) was reported to inhibit NAD kinase from Listeria monocytogenes and the crystal structure of the enzyme-inhibitor complex has been solved. We have synthesized tiazofurin adenosine disulfide (4) and the disulfide 5, and found that these compounds were moderate inhibitors of human NAD kinase (IC(50)=110 microM and IC(50)=87 microM, respectively) and Mycobacterium tuberculosis NAD kinase (IC(50)=80 microM and IC(50)=45 microM, respectively). We also found that NAD mimics with a short disulfide (-S-S-) moiety were able to bind in the folded (compact) conformation but not in the common extended conformation, which requires the presence of a longer pyrophosphate (-O-P-O-P-O-) linkage. Since majority of NAD-dependent enzymes bind NAD in the extended conformation, selective inhibition of NAD kinases by disulfide analogues has been observed. Introduction of bromine at the C8 of the adenine ring restricted the adenosine moiety of diadenosine disulfides to the syn conformation making it even more compact. The 8-bromoadenosine adenosine disulfide (14) and its di(8-bromoadenosine) analogue (15) were found to be the most potent inhibitors of human (IC(50)=6 microM) and mycobacterium NAD kinase (IC(50)=14-19 microM reported so far. None of the disulfide analogues showed inhibition of lactate-, and inosine monophosphate-dehydrogenase (IMPDH), enzymes that bind NAD in the extended conformation.
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Affiliation(s)
- Riccardo Petrelli
- Center for Drug Design, University of Minnesota, Minneapolis, MN 55455, USA
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24
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Aggelidou C, Mavridis IM, Yannakopoulou K. Binding of Nucleotides and Nucleosides to Per(6-guanidino-6-deoxy)cyclodextrins in Solution. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900040] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Neres J, Labello NP, Somu RV, Boshoff HI, Wilson DJ, Vannada J, Chen L, Barry CE, Bennett EM, Aldrich CC. Inhibition of siderophore biosynthesis in Mycobacterium tuberculosis with nucleoside bisubstrate analogues: structure-activity relationships of the nucleobase domain of 5'-O-[N-(salicyl)sulfamoyl]adenosine. J Med Chem 2008; 51:5349-70. [PMID: 18690677 DOI: 10.1021/jm800567v] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
5'-O-[N-(salicyl)sulfamoyl]adenosine (Sal-AMS) is a prototype for a new class of antitubercular agents that inhibit the aryl acid adenylating enzyme (AAAE) known as MbtA involved in biosynthesis of the mycobactins. Herein, we report the structure-based design, synthesis, biochemical, and biological evaluation of a comprehensive and systematic series of analogues, exploring the structure-activity relationship of the purine nucleobase domain of Sal-AMS. Significantly, 2-phenyl-Sal-AMS derivative 26 exhibited exceptionally potent antitubercular activity with an MIC99 under iron-deficient conditions of 0.049 microM while the N-6-cyclopropyl-Sal-AMS 16 led to improved potency and to a 64-enhancement in activity under iron-deficient conditions relative to iron-replete conditions, a phenotype concordant with the designed mechanism of action. The most potent MbtA inhibitors disclosed here display in vitro antitubercular activity superior to most current first line TB drugs, and these compounds are also expected to be useful against a wide range of pathogens that require aryl-capped siderphores for virulence.
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Affiliation(s)
- João Neres
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
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26
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Braendvang M, Gundersen LL. Synthesis, biological activity, and SAR of antimycobacterial 2- and 8-substituted 6-(2-furyl)-9-(p-methoxybenzyl)purines. Bioorg Med Chem 2007; 15:7144-65. [PMID: 17804243 DOI: 10.1016/j.bmc.2007.07.034] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Revised: 06/26/2007] [Accepted: 07/06/2007] [Indexed: 10/22/2022]
Abstract
A number of 6-(2-furyl)-9-(p-methoxybenzyl)purines carrying a variety of substituents in the 2- or 8-position have been synthesized and their ability to inhibit growth of Mycobacterium tuberculosis in vitro has been determined. It is demonstrated that sterical hindrance in the purine 8-position reduces activity and that C-8 should be unsubstituted. In the purine 2-position small, hydrophobic substituents are beneficial. The electronic properties of the 2-substituents appear to have only a minor influence on bioactivity. The compounds studied exhibit low toxicity toward mammalian cells (VERO cells) and are essentially inactive toward Staphylococcus aureus and Escherichia coli. The most active and selective antimycobacterial in the series detected to date is the novel 2-methyl-6-furyl-9-(p-methoxybenzyl)purine with MIC=0.20 microg/mL against M. tuberculosis and IC(50) against VERO cells >62.5 microg/mL. Also the novel 2-fluoro analog and the previously known 2-chloro compound, both with MIC=0.39 microg/mL, are highly interesting drug candidates.
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Affiliation(s)
- Morten Braendvang
- Department of Chemistry, University of Oslo, PO Box 1033, Blindern, N-0315 Oslo, Norway
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27
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Scott SP, Shea PW, Dryer SE. Mapping ligand interactions with the hyperpolarization activated cyclic nucleotide modulated (HCN) ion channel binding domain using a soluble construct. Biochemistry 2007; 46:9417-31. [PMID: 17655202 DOI: 10.1021/bi6026049] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hyperpolarization activated cyclic nucleotide modulated (HCN) ion channel currents are activated by hyperpolarization and modulated in response to changes in cytosolic adenosine 3',5'-cyclic monophosphate (cAMP) concentrations. A cDNA chimera combining the rat HCN2 cyclic nucleotide binding domain and the DNA binding domain of the cAMP receptor protein (CRP) from E. coli and the histidine tag (HCN2/CRP) was expressed and purified. The construct is capable of forming only non-ligand dependent dimers because the C-linker region of the channel is not present in this construct. The construct binds 8-[[2-[(fluoresceinylthioureido) amino] ethyl] thio] adenosine-3',5'-cyclic monophosphate (8-fluo cAMP) with a Kd of 0.299 microM as determined with a monomer binding model. The Ki values of 20 ligands related to cAMP were measured in order to determine the properties necessary for a ligand to bind to the HCN2 binding domain. This is the first report of cAMP and gunaosine 3',5'-cyclic monophosphate (cGMP) affinities to the HCN2 binding domain being equivalent, even though they modulate the channel with a 10-fold difference in K0.5. Furthermore, the array of ligands measured allows the preference rank order for each purine ring position to be determined: position 1, H > NH2 > O; position 2, NH2 > Cl > H > O; position 6, NH2 > Cl > H > O; and position 8, NH2 > Cl > H > O. Finally, the ability of HCN2/CRP to bind cyclic nucleotide pyrimidine rings at concentrations approximately 1.33 times greater than cAMP suggests that ribofuranose is key for binding.
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Affiliation(s)
- Sean-Patrick Scott
- Escuela de Medicine, Tec de Monterrey, Edificio CITES 3er piso, Area de Investigación, Av. Morones Prieto 3000 Pte., Col. Los Doctores, Monterrey, N.L. 64710, México.
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28
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van Galen PJ, Ijzerman AP, Soudijn W. Xanthine-7-Ribosides as Adenosine AlReceptor Antagonists: Further Evidence for Adenosine's Anti Mode of Binding. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319008045138] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Moreau C, Wagner GK, Weber K, Guse AH, Potter BVL. Structural determinants for N1/N7 cyclization of nicotinamide hypoxanthine 5'-dinucleotide (NHD+) derivatives by ADP-ribosyl cyclase from aplysia californica: Ca2+-mobilizing activity of 8-substituted cyclic inosine 5'-diphosphoribose analogues in T-lymphocytes. J Med Chem 2006; 49:5162-76. [PMID: 16913705 DOI: 10.1021/jm060275a] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of nicotinamide hypoxanthine 5'-dinucleotide (NHD+) analogues modified at C-8 (2-5) and 7-deaza-NHD+ were synthesized, and cyclization in the presence of Aplysia ADP-ribosyl cyclase was studied. All 8-substituted NHD+ analogues were converted into their N1-cyclic forms by the enzyme, while in contrast, 7-deaza-NHD+ 17 was hydrolyzed into 7-deazainosine 5'-diphosphoribose (7-deaza-IDPR) 25. Correlations are made showing that the conformation of the NHD+ substrate is the key to successful cyclization. The pharmacological activities of these novel cIDPR derivatives were evaluated in both permeabilized and intact Jurkat T-lymphocytes. The results show that in permeabilized cells both 8-iodo 1g and 8-N3-N1-cIDPR 1d have an activity comparable to that of cADPR, while 8-iodo 1g and 8-phenyl-N1-cIDPR 1c have a small but significant effect in intact cells and can therefore be regarded as membrane-permeant; thus, cIDPR derivatives are emerging as important novel biological tools to study cADPR-mediated Ca2+ release in T-cells.
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Affiliation(s)
- Christelle Moreau
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
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30
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Bookser BC, Matelich MC, Ollis K, Ugarkar BG. Adenosine Kinase Inhibitors. 4. 6,8-Disubstituted Purine Nucleoside Derivatives. Synthesis, Conformation, and Enzyme Inhibition. J Med Chem 2005; 48:3389-99. [PMID: 15857145 DOI: 10.1021/jm048968j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
6,8-Disubstituted purine nucleosides were synthesized and evaluated as adenosine kinase inhibitors (AKIs). A method was developed to selectively substitute arylamines for halogens at C6 and C8 which utilizes alkali salts of arylamino anions. Regioselectivity was found to be counterion dependent. Potassium and sodium salts add selectively to C6 of 6-chloro-8-iodo-9-(2,3,5-tris-O-tert-butyldimethylsilyl-beta-d-ribofuranosyl)purine (7a) while lithium salts add to C6 and C8 positions. Differential 6,8-bisarylamin-N,N'-diylpurine nucleosides such as 8-anilin-N-yl-6-indolin-N-yl-9-(beta-d-ribofuranosyl)purine (10b) can be prepared by employing stepwise reactions of potassium and then lithium salts of different arylamino anions followed by fluoride ion-induced desilylation. Other C8-substituted compounds were prepared by way of either C8 lithiation chemistry or palladium cross-coupling reactions. Several of these compounds were potent AKIs (e.g. 10b, AK IC(50) = 0.019 microM) and are more potent than the previous best purine-based AKI 5'-deoxy-5'-aminoadenosine (AK IC(50) = 0.170 microM). AK inhibitory potency was greatest for those compounds with (1)H NMR evidence of a predominant anti glycosyl bond conformation, whereas most analogues adopt a syn conformation because of steric repulsions between the C8 substituent and the ribose group. The inhibitors are proposed to bind in the anti conformation with the hydrophobic C6 and C8 substituents contributing to AK affinity in a manner similar to the C4 and C5 aryl substituents of the potent diaryltubercidin nucleoside inhibitor series.
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Affiliation(s)
- Brett C Bookser
- Metabasis Therapeutics, Inc., 9390 Towne Centre Drive, San Diego, California 92121, USA. bookser@ mbasis.com
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31
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Gannett PM, Heavner S, Daft JR, Shaughnessy KH, Epperson JD, Greenbaum NL. Synthesis, properties, and NMR studies of a C8-phenylguanine modified oligonucleotide that preferentially adopts the Z DNA conformation. Chem Res Toxicol 2004; 16:1385-94. [PMID: 14565779 DOI: 10.1021/tx034023d] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Carcinogenic aryl hydrazines produce C8-arylated purine adducts. The effect of these adducts on DNA conformation and their role in hydrazine carcinogenesis are unknown. Here, we describe a new synthetic route to produce these adducts that is also compatible with the synthesis of the corresponding phosphoramidites needed for oligonucleotide synthesis. Two oligonucleotides were prepared, an unmodified oligonucleotide, d((5)(')CGCGCGCGCG(3)(')), and a C8-phenylguanine modified oligonucleotide, d((5)(')CGCGCGCGCG(3)(')) (G = 8-phenylguanine). These oligonucleotides were compared using thermal denaturation, circular dichroism, NMR, and molecular modeling. The phenyl modification destabilizes the B DNA form and stabilizes the Z DNA form such that the B:Z ratio is near one under physiological conditions. In light of recent studies that show a role for Z DNA in gene expression and cell transformation, Z DNA stabilization by C8-arylguanine formation from aryl hydrazines may be relevant to their role in carcinogenesis.
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Affiliation(s)
- Peter M Gannett
- West Virginia University, P.O. Box 9530, Morgantown, West Virginia 26506, USA.
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32
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Cristalli G, Costanzi S, Lambertucci C, Taffi S, Vittori S, Volpini R. Purine and deazapurine nucleosides: synthetic approaches, molecular modelling and biological activity. FARMACO (SOCIETA CHIMICA ITALIANA : 1989) 2003; 58:193-204. [PMID: 12620415 DOI: 10.1016/s0014-827x(03)00019-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A number of ligands for the adenosine binding sites has been obtained by using nucleoside convergent and divergent synthesis. Most of our nucleosides have been synthesized by coupling 2,6-dichloropurine (1), 2,6-dichloro-1-deazapurine (2), 2,6-dichloro-3-deazapurine (3) with ribose, 2- and 3-deoxyribose and 2,3-dideoxyribose derivatives. The use of these versatile synthons allowed the introduction of various substituents in 2- and/or 6-positions. The glycosylation site and the anomeric configuration of the obtained nucleosides were assigned on the basis of spectroscopic studies and confirmed by molecular models. A series of potent adenosine receptor ligands has been obtained by using divergent approaches, mostly starting from guanosine. Substitutions in 2, 6, 8, and 5' position of adenosine molecule led to ligands selective for the different adenosine receptor subtypes. Furthermore, we investigated the molecular bases of the different behavior of 2- and 8-alkynyl adenosines, by means of NMR experiments and molecular modeling studies. With docking experiments, we demonstrated that the two class of molecules should have different binding modes that explain their different degree of affinity and the shift of their activity from agonistic (2-substituted derivatives) to antagonistic (8-substituted derivatives).
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Affiliation(s)
- Gloria Cristalli
- Dipartimento di Scienze Chimiche, Università di Camerino, via S Agostino 1, 62032 Camerino, MC, Italy.
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Costanzi S, Lambertucci C, Vittori S, Volpini R, Cristalli G. 2- and 8-alkynyladenosines: conformational studies and docking to human adenosine A3 receptor can explain their different biological behavior. J Mol Graph Model 2003; 21:253-62. [PMID: 12479925 DOI: 10.1016/s1093-3263(02)00161-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Adenosine (Ado) derivatives substituted at the C2 position with an alkynyl chain are endowed with high affinity for A(1), A(2A) and A(3) human adenosine receptors, while being less active at the low affinity A(2B) subtype. On the other hand, the introduction of an alkynyl chain at the C8 position of adenosine is detrimental for the affinity and potency at A(1), A(2A), and A(2B) receptors, while is more tolerated by the A(3) receptor. The evaluation of the stimulation of [35S]GTPgammaS binding revealed that 2-alkynyladenosines behave as adenosine receptors agonists while, on the contrary, 8-alkynyladenosines behave as antagonists. With this work we demonstrated, by means of an NMR-based and a computational conformational analysis, that 8-alkynyladenosines, differently from 2-alkynyladenosines, cannot adopt the sugar-base anti conformation required for adenosine receptor activation.Furthermore, using the recently reported X-ray crystal structure of bovine rhodopsin as template, we built a 3D model of the seven transmembrane domains of the human adenosine A(3) receptor with the homology modeling. After identification of the binding site we carried out docking experiments, demonstrating that the two class of molecules have different binding modes that explain their different degree of affinity and the shift of their activity from agonism to antagonism.
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Affiliation(s)
- Stefano Costanzi
- Dipartimento di Scienze Chimiche, Università di Camerino, 62032 Camerino, Italy
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Totsuka Y, Takamura-Enya T, Kawahara N, Nishigaki R, Sugimura T, Wakabayashi K. Structure of DNA adduct formed with aminophenylnorharman, being responsible for the comutagenic action of norharman with aniline. Chem Res Toxicol 2002; 15:1288-94. [PMID: 12387627 DOI: 10.1021/tx020007p] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A mutagenic heterocyclic amine (HCA), 9-(4'-aminophenyl)-9H-pyrido[3,4-b]indole (aminophenylnorharman, APNH), is produced in the presence of S9 mix by the reaction of norharman and aniline, both of which are nonmutagenic and abundantly present in our environment. It has been previously reported that APNH-DNA adducts were detected in DNA of Salmonella typhimurium strain incubated with APNH and S9 mix. In the present study, we examined the structures of APNH-DNA adducts using the (32)P-postlabeling method and various spectrometry techniques. When the reaction mixture of N-acetoxy-APNH and 2'-deoxyguanosine 3'-monophosphate (3'-dGp) was analyzed, three adduct spots (two major and one minor) were observed by (32)P-postlabeling under modified-standard conditions. No adduct formation was observed for reaction mixtures of N-acetoxy-APNH with 3'-dAp, 3'-dTp, or 3'-dCp. The two major adduct spots (spots 1 and 2) detected by TLC were extracted and subjected to HPLC along with the standards 3',5'-pdGp-C8-APNH and 5'-pdG-C8-APNH, which were independently chemically synthesized. On the basis of the results of co-chromatography, spots 1 and 2 were identified to be 5'-monophosphate and 3',5'-diphosphate forms of dG-C8-APNH. When the extract of spot 2 (3',5'-pdGp-C8-APNH) was further digested with nuclease P1 and phosphodiesterase I, a spot corresponding to spot 1 (5'-pdG-C8-APNH) was newly observed on TLC. From these observations, both of the two major spots were concluded to be dG-C8-APNH. A similar DNA adduct pattern to that apparent in vitro was observed in various organs of F344 rats fed 40 ppm of APNH for 4 weeks. The levels of APNH-DNA adducts were highest in the liver and colon, with RAL values of 1.31 +/- 0.26 and 1.32 +/- 0.11 adducts/10(7)nucleotides, respectively. Thus, APNH was demonstrated to form DNA adducts primarily at the C-8 position of guanine residues in vitro and in vivo, like other mutagenic and carcinogenic HCAs.
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Affiliation(s)
- Yukari Totsuka
- Cancer Prevention Division, National Cancer Center Research Institute, 1-1 Tsukiji 5-chome, Chuo-ku, Tokyo 104-0045, Japan
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Minelli A, Moroni M, Mezzasoma I, Skladanowski AC. Activity of IMP- and AMP-preferring isoforms of 5'-nucleotidase from human seminal plasma with AMP analogues. Mol Genet Metab 1999; 66:49-55. [PMID: 9973547 DOI: 10.1006/mgme.1998.2769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
AMP analogues modified at various positions of the molecule were checked as substrates for the two soluble isoforms of 5'-nucleotidase from human seminal plasma. These isoforms were isolated to near homogeneity by affinity chromatographies. AMP derivatives were differently dephosphorylated by both the isoforms depending on the site of modification in the natural compound. Changes in the phosphate moiety reduced significantly hydrolysis by the IMP-preferring form, whereas the AMP-preferring form was less affected. The AMP-preferring form was characterized by a relatively broad specificity toward substrate analogues indicating that the binding domains for the phosphate moiety of these isoforms are not identical. Substitutions at the C-8 adenine base reduced the hydrolysis rate of both the enzymes and variations of the syn-anti conformational equilibrium resulted in different effects on catalysis by both forms. Therefore, the orientation of the heterocyclic base around the glycosidic bond may not be the crucial factor affecting binding and catalytic activity. Hydrogen bonding potential of base N-7 was essential for the binding and catalysis of the IMP- but not of the AMP-preferring form. This was the most striking difference between the studied isoforms. Modifications and substitutions of 6-amino function, better accepted by the IMP-preferring form than by the AMP-preferring form, indicated that no essential hydrogen bonding is required for catalytic activity. The binding was however significantly slowed in 6-SH-PuMP. Hydrogen bonding potential of N-1 was significant for the hydrolysis rate of the IMP- but not of the AMP-preferring form. We suggest that these human seminal plasma isoforms of soluble 5'-nucleotidase, characterized by unique features, may represent the tissue-specific expression of the polymorphic gene.
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Affiliation(s)
- A Minelli
- Sezione di Enzimologia, Università degli Studi di Perugia, Perugia, 06123, Italy
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Enya T, Kawanishi M, Suzuki H, Matsui S, Hisamatsu Y. An unusual DNA adduct derived from the powerfully mutagenic environmental contaminant 3-nitrobenzanthrone. Chem Res Toxicol 1998; 11:1460-7. [PMID: 9860488 DOI: 10.1021/tx980104b] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The covalent binding of an N-hydroxy metabolite of the powerfully mutagenic 3-nitrobenzanthrone (NBA) to 2'-deoxyguanosine (dG) and calf thymus DNA has been investigated in vitro. The major adduct obtained from the reaction of the N-acetoxy-N-acetyl derivative (N-Aco-N-Ac-ABA) of 3-aminobenzanthrone (ABA) and dG was identified as N-acetyl-3-amino-2-(2'-deoxyguanosin-8-yl)benzanthrone (dG-N-Ac-ABA) by 1H NMR and mass spectroscopies as well as by the reaction of N-Aco-N-Ac-ABA with the double-stranded calf thymus DNA. The coupling with the dG moiety occurred exclusively at C-2 of benzanthrone (BA), suggesting a significant contribution of a resonance-stabilized arenium ion intermediate derived from BA to the production of this new type of adduct. The preferred conformation of the adduct has been shown to be syn by 1H and 13C NMR.
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Affiliation(s)
- T Enya
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan. Community Environmental Science
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Marques MM, Mourato LL, Amorim MT, Santos MA, Melchior WB, Beland FA. Effect of substitution site upon the oxidation potentials of alkylanilines, the mutagenicities of N-hydroxyalkylanilines, and the conformations of alkylaniline-DNA adducts. Chem Res Toxicol 1997; 10:1266-74. [PMID: 9403181 DOI: 10.1021/tx970104w] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Carcinogenic arylamines typically undergo metabolic activation via N-hydroxylation followed in most instances by O-esterification. In this study, the ability of methyl-, dimethyl-, and ethylaniline constituents of tobacco smoke to undergo oxidation at the nitrogen atom was analyzed. In addition, the mutagenicity of the corresponding N-hydroxyalkylanilines and the conformational properties of the DNA adducts generated from their N-acyloxy derivatives were investigated. All the arylamines underwent irreversible electrochemical N-oxidation at potentials higher than those observed for the oxidation of carcinogenic polynuclear aromatic amines. There were minor differences in the oxidation potentials, which were consistent with the position and electron-donating abilities of the alkyl substituents; however, the differences appeared to be too small to account for the range of genotoxic effects among the alkylanilines. N-Hydroxyarylamines containing p-alkyl substituents had increased mutagenicities in Salmonella typhimurium TA100, which was attributed to their higher efficiencies of adduct formation. Increased mutagenicities were also observed upon o-alkyl substitution; however, this property was not related to a greater ability of the ortho-substituted species to form DNA adducts, which suggested that adducts from ortho-substituted alkylanilines may be intrinsically more mutagenic than their meta- and para-substituted analogues. In all instances, N-(acyloxy)-arylamines generated from the N-hydroxyarylamines reacted with dG, dG nucleotides, and DNA to yield C8-substituted dG derivatives as the major adducts. The alkylaniline-dG adducts displayed distinct conformational trends that were determined by the location of the alkyl substituents. Spectroscopic data indicated higher percentages of low-energy syn conformers in the adducts that contained alkyl groups ortho to the arylamine nitrogen as opposed to adducts not bearing ortho substituents. The data strongly suggest that the conformational properties of the DNA adducts, in particular their ability to adopt syn conformations, may be determinant factors for the genotoxic responses elicited by certain alkylanilines (e.g., 2-methylaniline and 2,6-dimethylaniline).
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Affiliation(s)
- M M Marques
- Centro de Química Estrutural, Instituto Superior Técnico, Lisboa, Portugal
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Beland FA, Melchior WB, Mourato LL, Santos MA, Marques MM. Arylamine-DNA adduct conformation in relation to mutagenesis. Mutat Res 1997; 376:13-9. [PMID: 9202733 DOI: 10.1016/s0027-5107(97)00020-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A considerable body of evidence has indicated that local conformational alterations induced by DNA adducts may provide the molecular basis for differences in mutational specificities exhibited by structurally similar adducts. To elucidate the relationships between adduct structure and mutation induction, the ability of several single-ring arylamines present in tobacco smoke (i.e., methylanilines, dimethylanilines, and ethylanilines) to form DNA adducts was investigated. In all cases, the major adducts were C8-substituted deoxyguanosine derivatives, which is consistent with what has been observed with more carcinogenic arylamines, such as 2-aminofluorene and 4-aminobiphenyl. Spectroscopic and theoretical data on the adducts indicated conformational differences depending upon the location of the alkyl substituents. Adducts containing alkyl groups ortho to the amino function (e.g., 2-methylaniline) had a greater percentage of syn conformers about the glycosyl bond than those not bearing such groups. Arylamines with ortho alkyl substituents tend to be more mutagenic and tumorigenic than analogues not containing an ortho alkyl substituent. This increase in biological activity may be due in part to the greater propensity of ortho alkylated adducts to adopt a syn conformation.
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Affiliation(s)
- F A Beland
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR 72079, USA.
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40
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Gannett PM, Lawson T, Miller M, Thakkar DD, Lord JW, Yau WM, Toth B. 8-Arylguanine adducts from arenediazonium ions and DNA. Chem Biol Interact 1996; 101:149-64. [PMID: 8760396 DOI: 10.1016/0009-2797(96)03722-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Arenediazonium ions (ArN2+) are genotoxic though the source of their genotoxicity is unknown. The present studies were undertaken to determine if reductive decomposition of ArN2+ to aryl radicals (Ar) in the presence of calf thymus DNA (ctDNA) or in cells results in the formation of DNA adducts. We found that when arenediazonium ions of the general structure p-X-ArN2+ (X = CH3, CH2OCH3, CH2OH) are allowed to react with ctDNA or incubated with cells under conditions that produce p-X-Ar, DNA adducts are formed with guanine. The structure of the adduct is the C8-substitution product derived from guanine and p-X-Ar. Formation of p-X-Ar was determined by ESR spin-trapping with 5,5-dimethyl-1-pyrroline N-oxide (DMPO). The extent of C8-arylguanine adduction was measured by high performance liquid chromatography (HPLC) analysis of the DNA hydrosylate and comparison with authentic synthetic standards. The C8-arylguanine adducts observed to form may be important in regard to the genotoxicity of ArN2+, though other DNA adducts such as the N6-triazene of adenine or C8-aryladenine adducts can form. Finally, though the formation of C8-arylguanine adducts from arenediazonium ions has been proposed, this is the first report demonstrating their formation in DNA.
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Affiliation(s)
- P M Gannett
- West Virginia University, School of Pharmacy, Morgantown 26506, USA.
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Marques MM, Mourato LL, Santos MA, Beland FA. Synthesis, characterization, and conformational analysis of DNA adducts from methylated anilines present in tobacco smoke. Chem Res Toxicol 1996; 9:99-108. [PMID: 8924623 DOI: 10.1021/tx950044z] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The ability of a series of aromatic amines present in tobacco smoke (2-, 3-, and 4-methylaniline, 2,3- and 2,4-dimethylaniline) to bind to DNA has been investigated by reacting N-(acyloxy)arylamines with dG, dG nucleotides, and DNA. The predominant products from reactions with dG and the nucleotides were characterized as N-(deoxyguanosin-8-yl)arylamines by spectroscopic and HPLC methods. HPLC and spectroscopic analyses of the modified DNA indicated the same adducts. Analyses of the 1H and 13C NMR spectra suggested that the adducts containing a methyl substituent ortho to the arylamine nitrogen had a higher percentage of syn conformers. This observation was supported by theoretical simulation studies that indicated substantial percentages of low energy syn conformers, increasing with the substitution pattern in the order para < meta < ortho < ortho,para < ortho,meta. The results demonstrate that, although single-ring arylamines are considered weak carcinogens, their electrophilic N-acetoxy derivatives, which are plausible metabolic intermediates, react with DNA to yield covalent adducts structurally identical to those derived from carcinogenic polyarylamines, such as 2-aminofluorene and 4-aminobiphenyl. Furthermore, the conformational perturbation induced in DNA by the formation of the monoarylamine-DNA adducts, especially those with an ortho substituent, may contribute to the biological activities of these compounds.
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Affiliation(s)
- M M Marques
- Centro de Química Estrutural, Instituto Superior Técnico, Lisboa, Portugal
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Van der Wenden EM, Hartog-Witte HR, Roelen HC, von Frijtag Drabbe Künzel JK, Pirovano IM, Mathôt RA, Danhof M, Van Aerschot A, Lidaks MJ, IJzerman AP. 8-substituted adenosine and theophylline-7-riboside analogues as potential partial agonists for the adenosine A1 receptor. Eur J Pharmacol 1995; 290:189-99. [PMID: 7589213 DOI: 10.1016/0922-4106(95)00064-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A series of 8-substituted adenosine and theophylline-7-riboside analogues (28 and 9 compounds, respectively) was tested on adenosine A1 and A2A receptors as an extensive exploration of the adenosine C8-region. Alkylamino substituents at the 8-position cause an affinity decrease for adenosine analogues, but an affinity increase for theophylline-7-riboside derivatives. The affinity decrease is probably due to a direct steric hindrance between the C8-substituent and the binding site as well as to electronic effects, not to a steric influence on the ribose moiety to adopt the anti conformation. The 8-substituents increase the affinity of theophylline-7-riboside analogues probably by binding to a lipophilic binding site. The intrinsic activity was tested in vitro for some 8-substituted adenosine analogues, by determining the GTP shift in receptor binding studies and the inhibition of adenylate cyclase in a culture of rat thyroid FRTL-5 cells, and in vivo in the rat cardiovascular system for 8-butylaminoadenosine. Thus, it was shown that 8-ethyl-, 8-butyl-, and 8-pentylamino substituted analogues of adenosine may be partial agonists in vitro, and that 8-butylaminoadenosine is a partial agonist for the rat cardiovascular A1 receptor in vivo.
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Affiliation(s)
- E M Van der Wenden
- Division of Medicinal Chemistry, Leiden-Amsterdam Center for Drug Research, Leiden University, The Netherlands
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Bzowska A, Kulikowska E, Shugar D. Formycins A and B and some analogues: selective inhibitors of bacterial (Escherichia coli) purine nucleoside phosphorylase. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1120:239-47. [PMID: 1576149 DOI: 10.1016/0167-4838(92)90243-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Formycin B (FB), a moderate inhibitor (Ki approximately 100 microM) of mammalian purine nucleoside phosphorylase (PNP), and formycin A (FA), which is totally inactive vs. the mammalian enzyme, are both effective inhibitors of the bacterial (Escherichia coli) enzyme (Ki approximately 5 microM). Examination of a series of N-methyl analogues of FA and FB led to the finding that N(6)-methyl-FA, virtually inactive vs. the mammalian enzyme, is the most potent inhibitor of E. coli purine nucleoside phosphorylase (Ki approximately 0.3 uM) at neutral pH. Inhibition is competitive not only with respect to Ino, but also relative to 7-methyl-Guo and 7-methyl-Ado, as substrates. Both oxoformycins A and B are relatively poor inhibitors. For the most potent inhibitor, N(6)-methyl-FA, it was shown that the enzyme preferentially binds the neutral, and not the cationic, form. In accordance with this the neutral, but not the cationic form, of the structurally related N(1)-methyl-Ado was found to be an excellent substrate. Reported data on tautomerism of formycins were profited from, and extended, to infer which tautomeric species and ionic forms are the active inhibitors. A commercially available (Sigma) bacterial PNP, of unknown origin, was shown to differ from the E. coli enzyme by its inability to phosphorylase Ado; this enzyme was also resistant to FA and FB. These findings have been extended to provide a detailed comparison of the substrate/inhibitor properties of PNP from various microorganisms.
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Affiliation(s)
- A Bzowska
- Department of Biophysics, University of Warsaw, Poland
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44
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Cho BS, Evans FE. Correlation between NMR spectral parameters of nucleosides and its implication to the conformation about the glycosyl bond. Biochem Biophys Res Commun 1991; 180:273-8. [PMID: 1930225 DOI: 10.1016/s0006-291x(05)81288-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Analyses of high resolution proton and carbon NMR spectra of a series of guanine nucleosides in DMSO have revealed a near linear correlation between the chemical shift of the H2, atom of the sugar moiety and the vicinal coupling constant 3JC4-H1'. This unexpected result provides evidence that the variations in the glycosyl torsion angle between nucleosides in solution are less that those which have previously been reported in crystals and it is an experimental basis for analyzing the syn and anti populations from chemical shift and coupling constant data.
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Affiliation(s)
- B S Cho
- Division of Biochemical Toxicology, Food and Drug Administration, Jefferson, Arkansas 72079
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Niedzwicki JG, Abernethy DR. Structure-activity relationship of ligands of human plasma adenosine deaminase2. Biochem Pharmacol 1991; 41:1615-24. [PMID: 2043151 DOI: 10.1016/0006-2952(91)90162-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Diethylaminoethyl-cellulose chromatography was used to separate the two isoenzymes of adenosine deaminase (EC3.5.4.4), adenosine deaminase1 (ADA1) and adenosine deaminase2 (ADA2), in human plasma. One hundred and fifteen purine base, nucleoside, and nucleotide analogs were tested as inhibitors of this partially purified preparation of ADA2. Coformycin and 2'-deoxycoformycin were by far the most potent inhibitors of this isoenzyme (apparent Ki values 20 and 19 nM, respectively). ADA2 was also inhibited by nebularine (apparent Ki 1.5 mM) but was resistant to the potent ADA1 inhibitor (+)-erythro-9(2-S-hydroxy-3-R-nonyl)adenine. alpha-D-Adenosine also inhibited ADA2, as did several halogenated purine and adenine base analogs. Structural requirements for the binding of purine analogs to ADA2 are presented which provide a general basis for the design of specific inhibitors of ADA2. Such inhibitors may be useful in studies designed to provide an understanding of the physiological role of ADA2 both in the normal state and in diseases such as human immunodeficiency virus-1 infection where levels in plasma are increased markedly.
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Affiliation(s)
- J G Niedzwicki
- Division of Clinical Pharmacology, Brown University, Providence, Rhode Island
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46
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Meier C, Boche G. 1H- und13C-NMR-Konformationsanalysen und Minimal-Potential-Energie-Rechnungen an Desoxyguanosin-, Guanosin- und 5′-Guanosinmonophosphat-Addukten des Grenzcarcinogens 4-Methylanilin. ACTA ACUST UNITED AC 1990. [DOI: 10.1002/cber.19901230821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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47
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Abstract
The specificity of the ATP-binding site of rhodopsin kinase was studied with adenosine analogues that are competitive inhibitors. Systematic changes in the ribose ring (position 5') and the purine ring (positions 2, 6, 7, 8, and 9) and determination of the inhibitory properties of these analogues lead to the following conclusions: (1) The N6 nitrogen in the purine ring is essential for binding at the active site, which may explain the marked preference for ATP rather than GTP as substrate. (2) The configuration of the sugar moiety is critical for the binding. (3) Positions 2, 3, and 8 of the purine ring, as well as the polyphosphate chain, play a minor role in substrate recognition by rhodopsin kinase. (4) ATP gamma S is a good substrate for rhodopsin kinase (thus rhodopsin phosphorothioate, a phosphatase-resistant product, can be formed in order to study the role of phosphorylation in rod outer segments). Pyrrolopyrimidine derivatives are very potent inhibitors of rhodopsin kinase. The Ki of one of these, sangivamycin, is 180 nM. Sangivamycin in solution assumes the anti conformation, as determined by nuclear Overhauser measurement. These measurements show that the most potent inhibitors of rhodopsin kinase, sangivamycin and toyocamycin, occur in solution preferentially in the anti conformation. Many nucleotides and nucleosides tested that are not inhibitors are syn, and many that are inhibitors form a mixture of syn and anti. The hypothesis that inhibitors may have a conformation intermediate between syn and anti was strengthened by testing a cyclic nucleoside locked in an anti conformation.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- K Palczewski
- Department of Ophthalmology, University of Florida, Gainesville 32610
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48
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Goya P, Martinez A, Jimeno ML. Rotational isomerism in 6-β-D-glucopyranosides of methyl-1,2,6-thiadiazin-3(2H)-one 1,1-dioxides. ACTA ACUST UNITED AC 1990. [DOI: 10.1039/p29900000783] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Buckin VA, Kankiya BI, Kazaryan RL. Hydration of nucleosides in dilute aqueous solutions. Ultrasonic velocity and density measurements. Biophys Chem 1989; 34:211-23. [PMID: 2482087 DOI: 10.1016/0301-4622(89)80060-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The values of the concentration increments of the ultrasound velocity and their temperature slopes, apparent molar volumes, apparent molar expansibilities, apparent molar adiabatic compressibilities and their temperature gradients for 12 nucleosides and their analogs, as well as for ribose and deoxyribose, have been obtained using precision measurements of ultrasound velocity and density. The following hydration parameters for the atomic groups of the nucleosides, reflecting the state of water in the hydration shells of these groups, have been analyzed: (1) the contribution of ribose to the values of the concentration increment of ultrasound velocity A, the apparent molar volumes phi v and apparent molar adiabatic compressibilities phi ks of nucleosides; (2) contributions of the CH3, NH2 and O = ... -H groups of nucleic bases to the A, phi v and phi ks values of nucleosides and free nucleic bases; (3) contributions of the 2'-OH group of ribose to the values of A, phi v and phi ks nucleosides; (4) changes in the A values of nucleosides and free nucleic bases upon their protonation and deprotonation. Data have been obtained on the mutual influence of the atomic groups of nucleosides on their hydration. It is shown that the GC pairs of free deoxynucleosides undergo hydration more vigorously than the AT pairs, which contrasts with the relation of the degree of hydration of the GC and AT pairs of the double helix.
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Affiliation(s)
- V A Buckin
- Institute of Biological Physics, Academy of Sciences of the U.S.S.R., Moscow Region
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Moos WH, Hamilton HW, Ortwine DF, Taylor MD, McPhail AT. Adenosine Receptor Agonists. X-Ray Crystal Structure of Neca 1-(6-Amino-9H-Purin-9-Yl)-1-Deoxy-N-Ethyl-β-D-Ribofuranuronamide. ACTA ACUST UNITED AC 1989. [DOI: 10.1080/07328318908054188] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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