1
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Yakovleva EY, Patrushev YV, Shundrina IK, Glazneva TS. Properties of chromatographic columns prepared on the basis of poly(1-trimethylsilyl-1-propyne) modified with organic bases. J Chromatogr A 2024; 1723:464914. [PMID: 38640880 DOI: 10.1016/j.chroma.2024.464914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 04/21/2024]
Abstract
This article describes the effect of modification with organic bases such as uracil (U) and polyethyleneimine (PEI) on the adsorption and chromatographic properties of poly(1-trimethylsilyl-1-propyne) (PTMSP) used as a stationary phase (SP) in packed and capillary columns. It was shown that the sorbents prepared on the basis of diatomite Chromosorb P NAW support and successively modified with 9 wt.% PTMSP and 1 wt.% U (or PEI) (PC-U and PC-PEI samples, respectively), have a mesoporous structure. The IR spectrum shows the presence of carbonyl groups in the sorbent modified with uracil. The impregnation of the Chromosorb P NAW + (9/1) wt.% PTMSP sorbent with a polyethyleneimine solution leads to the appearance in the spectrum of bands characterizing NH stretching and bending vibrations, as well as a band at 1310 cm-1 which can be attributed to CN bond vibrations. The chromatographic properties of the studied sorbents differ significantly from the properties of the initial PTMSP. Packed columns PC-U and PC-PEI, as well as capillary columns with a polyethyleneimine-modified PTMSP layer, allow one to selectively separate mixtures of polar and non-polar compounds and structural isomers of hydrocarbons. Methanol on these columns is eluted in the form of a symmetrical peak separately from propane, propylene and other associated hydrocarbon impurities in commercial (technical, target) n-butane.
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Affiliation(s)
- Elena Y Yakovleva
- Boreskov Institute of Catalysis, pr. Lavrentieva 5, Novosibirsk 630090, Russia; Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia.
| | - Yuri V Patrushev
- Boreskov Institute of Catalysis, pr. Lavrentieva 5, Novosibirsk 630090, Russia; Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia
| | - Inna K Shundrina
- N.N. Vorozhtsov Institute of Organic Chemistry, pr. Lavrentieva 9, Novosibirsk 630090, Russia
| | - Tatiana S Glazneva
- Boreskov Institute of Catalysis, pr. Lavrentieva 5, Novosibirsk 630090, Russia
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2
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Orndorff PB, van der Vaart A. Systematic assessment of the flexibility of uracil damaged DNA. J Biomol Struct Dyn 2024; 42:3958-3968. [PMID: 37261803 DOI: 10.1080/07391102.2023.2217683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]
Abstract
Uracil is a common DNA lesion which is recognized and removed by uracil DNA-glycosylase (UDG) as a part of the base excision repair pathway. Excision proceeds by base flipping, and UDG efficiency is thought to depend on the ease of deformability of the bases neighboring the lesion. We used molecular dynamics simulations to assess the flexibility of a large library of dsDNA strands, containing all tetranucleotide motifs with U:A, U:G, T:A or C:G base pairs. Our study demonstrates that uracil damaged DNA largely follows trends in flexibility of undamaged DNA. Measured bending persistence lengths, groove widths, step parameters and base flipping propensities demonstrate that uracil increases the flexibility of DNA, and that U:G base paired strands are more flexible than U:A strands. Certain sequence contexts are more deformable than others, with a key role for the 3' base next to uracil. Flexibilities are large when this base is an A or G, and repressed for a C or T. A 5' T adjacent to the uracil strongly promotes flexibility, but other 5' bases are less influential. DNA bending is correlated to step deformations and base flipping, and bending aids flipping. Our study implies that the link between substrate flexibility and UDG efficiency is widely valid, helps explain why UDG prefers to bind U:G base paired strands, and suggests that the DNA bending angle of the UDG-substrate complex is optimal for base flipping.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Paul B Orndorff
- Department of Chemistry, University of South Florida, Tampa, Florida, USA
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3
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Parikh S, Limbachiya C. Electron interaction with DNA constituents in aqueous phase. Chemphyschem 2024; 25:e202300916. [PMID: 38259215 DOI: 10.1002/cphc.202300916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 01/24/2024]
Abstract
Electron driven chemistry of biomolecules in aqueous phase presents the realistic picture to study molecular processes. In this study we have investigated the interactions of electrons with the DNA constituents in their aqueous phase in order to obtain the quantities useful for DNA damage assessment. We have computed the inelastic mean free path (IMFP), mass stopping power (MSP) and absorbed dose (D) for the DNA constituents (Adenine, Cytosine, Guanine, Thymine and Uracil) in the aqueous medium from ionisation threshold to 5000 eV. We have modified complex optical potential formalism to include band gap of the systems to calculate inelastic cross sections which are used to estimate these entities. This is the maiden attempt to report these important quantities for the aqueous DNA constituents. We have compared our results with available data in gas and other phase and have observed explicable accord for IMFP and MSP. Since these are the first results of absorbed dose (D) for these compounds, we have explored present results vis-a-vis dose absorption in water.
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Affiliation(s)
- Smruti Parikh
- The Maharaja Sayajirao University of Baroda, Vadodara, 390 001
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4
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Guo B, Hu C, Yang Z, Tang C, Zhang C, Wang F. Test strip coupled Cas12a-assisted signal amplification strategy for sensitive detection of uracil-DNA glycosylase. Lab Chip 2024; 24:1987-1995. [PMID: 38372397 DOI: 10.1039/d4lc00096j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Uracil-DNA glycosylase (UDG) is a base excision repair (BER) enzyme, which catalyzes the hydrolysis of uracil bases in DNA chains that contain uracil and N-glycosidic bonds of the sugar phosphate backbone. The expression of UDG enzyme is associated with a variety of genetic diseases including cancers. Hence, the identification of UDG activity in cellular processes holds immense importance for clinical investigation and diagnosis. In this study, we employed Cas12a protein and enzyme-assisted cycle amplification technology with a test strip to establish a precise platform for the detection of UDG enzyme. The designed platform enabled amplifying and releasing the target probe by reacting with the UDG enzyme. The amplified target probe can subsequently fuse with crRNA and Cas12a protein, stimulating the activation of the Cas12a protein to cleave the signal probe, ultimately generating a fluorescent signal. This technique showed the ability for evaluating UDG enzyme activity in different cell lysates. In addition, we have designed a detection probe to convert the fluorescence signal into test strip bands that can then be observed with the naked eye. Hence, our tool presented potential in both biomedical research and clinical diagnosis related to DNA repair enzymes.
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Affiliation(s)
- Bin Guo
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an 710071, China
| | - Chong Hu
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an 710071, China
| | - Zeping Yang
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an 710071, China
| | - Chu Tang
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an 710071, China
| | - Chuanxian Zhang
- Institute of Medical Engineering, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Fu Wang
- Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an 710071, China
- Institute of Medical Engineering, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an 710061, China.
- Xianyang Key Laboratory of Molecular Imaging and Drug Synthesis, School of Pharmacy, Shaanxi Institute of International Trade & Commerce, Xianyang 712046, China
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5
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Chowdhury M, Turner JA, Cappello D, Hajjami M, Hudson RHE. Chimeric GFP-uracil based molecular rotor fluorophores. Org Biomol Chem 2023; 21:9463-9470. [PMID: 37997774 DOI: 10.1039/d3ob01539d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Uracil has been modified at the 5-position to derive a small library of nucleobase-chromophores which were inspired by green fluorescent protein (GFP). The key steps in the syntheses were Erlenmeyer azlactone synthesis followed by amination by use of hexamethyl disilazane (HMDS) to produce the imidazolinone derivatives. The uracil analogues displayed emission in the green region of visible spectrum and exhibited microenvironmental sensitivity exemplified by polarity-based solvatochromism and viscosity-dependent emission enhancement. Solid-state quantum yields of approximately 0.2 and solvent dependent emission wavelengths beyond 500 nm were observed. Select analogues were incorporated into peptide nucleic acid (PNA) strands which upon duplex formation with DNA showed good response ranging from a turn-off of fluorescence in presence of an opposing mismatched residue to a greater than 3-fold turn-on of fluorescence upon binding to fully complementary DNA strand.
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Affiliation(s)
- Mria Chowdhury
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7. rhhudson@uwo
| | - Julia A Turner
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7. rhhudson@uwo
| | - Daniela Cappello
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7. rhhudson@uwo
| | - Maryam Hajjami
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7. rhhudson@uwo
| | - Robert H E Hudson
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7. rhhudson@uwo
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6
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de Vries I, Ammerlaan D, Heidebrecht T, Celie PH, Geerke DP, Joosten RP, Perrakis A. Distant sequence regions of JBP1 contribute to J-DNA binding. Life Sci Alliance 2023; 6:e202302150. [PMID: 37328191 PMCID: PMC10276184 DOI: 10.26508/lsa.202302150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/18/2023] Open
Abstract
Base-J (β-D-glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J-binding protein 1 (JBP1) that has a thymidine hydroxylase domain and a J-DNA-binding domain (JDBD). How the thymidine hydroxylase domain synergizes with the JDBD to hydroxylate thymine in specific genomic sites, maintaining base-J during semi-conservative DNA replication, remains unclear. Here, we present a crystal structure of the JDBD including a previously disordered DNA-contacting loop and use it as starting point for molecular dynamics simulations and computational docking studies to propose recognition models for JDBD binding to J-DNA. These models guided mutagenesis experiments, providing additional data for docking, which reveals a binding mode for JDBD onto J-DNA. This model, together with the crystallographic structure of the TET2 JBP1-homologue in complex with DNA and the AlphaFold model of full-length JBP1, allowed us to hypothesize that the flexible JBP1 N-terminus contributes to DNA-binding, which we confirmed experimentally. Α high-resolution JBP1:J-DNA complex, which must involve conformational changes, would however need to be determined experimentally to further understand this unique underlying molecular mechanism that ensures replication of epigenetic information.
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Affiliation(s)
- Ida de Vries
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Danique Ammerlaan
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tatjana Heidebrecht
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Patrick Hn Celie
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan P Geerke
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS) and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Robbie P Joosten
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anastassis Perrakis
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
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7
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Buckley RJ, Lou‐Hing A, Hanson KM, Ahmed NR, Cooper CDO, Bolt EL. Escherichia coli DNA repair helicase Lhr is also a uracil-DNA glycosylase. Mol Microbiol 2023; 120:298-306. [PMID: 37452011 PMCID: PMC10953399 DOI: 10.1111/mmi.15123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
DNA glycosylases protect genetic fidelity during DNA replication by removing potentially mutagenic chemically damaged DNA bases. Bacterial Lhr proteins are well-characterized DNA repair helicases that are fused to additional 600-700 amino acids of unknown function, but with structural homology to SecB chaperones and AlkZ DNA glycosylases. Here, we identify that Escherichia coli Lhr is a uracil-DNA glycosylase (UDG) that depends on an active site aspartic acid residue. We show that the Lhr DNA helicase activity is functionally independent of the UDG activity, but that the helicase domains are required for fully active UDG activity. Consistent with UDG activity, deletion of lhr from the E. coli chromosome sensitized cells to oxidative stress that triggers cytosine deamination to uracil. The ability of Lhr to translocate single-stranded DNA and remove uracil bases suggests a surveillance role to seek and remove potentially mutagenic base changes during replication stress.
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Affiliation(s)
| | - Anna Lou‐Hing
- School of Life SciencesUniversity of NottinghamNottinghamUK
| | - Karl M. Hanson
- School of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK
| | - Nadia R. Ahmed
- School of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK
| | - Christopher D. O. Cooper
- School of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK
- CHARM Therapeutics LtdB900 Babraham Research CampusCambridgeUK
| | - Edward L. Bolt
- School of Life SciencesUniversity of NottinghamNottinghamUK
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8
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Zhao C, Arroyo-Mora LE, DeCaprio AP, Dionysiou DD, O'Shea KE, Sharma VK. Ferrate(VI) mediated degradation of the potent cyanotoxin, cylindrospermopsin: Kinetics, products, and toxicity. Water Res 2023; 233:119773. [PMID: 36870108 DOI: 10.1016/j.watres.2023.119773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 02/13/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
The presence of cylindrospermopsin (CYN), a potent cyanotoxin, in drinking water sources poses a tremendous risk to humans and the environment. Detailed kinetic studies herein demonstrate ferrate(VI) (FeVIO42-, Fe(VI)) mediated oxidation of CYN and the model compound 6-hydroxymethyl uracil (6-HOMU) lead to their effective degradation under neutral and alkaline solution pH. A transformation product analysis indicated oxidation of the uracil ring, which has functionality critical to the toxicity of CYN. The oxidative cleavage of the C5=C6 double bond resulted in fragmentation of the uracil ring. Amide hydrolysis is a contributing pathway leading to the fragmentation of the uracil ring. Under extended treatment, hydrolysis, and extensive oxidation lead to complete destruction of the uracil ring skeleton, resulting in the generation of a variety of products including nontoxic cylindrospermopsic acid. The ELISA biological activity of the CYN product mixtures produced during Fe(VI) treatment parallels the concentration of CYN. These results suggest the products do not possess ELISA biological activity at the concentrations produced during treatment. The Fe(VI) mediated degradation was also effective in the presence of humic acid and unaffected by the presence of common inorganic ions under our experimental conditions. The Fe(VI) remediation of CYN and uracil based toxins appears a promising drinking water treatment process.
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Affiliation(s)
- Cen Zhao
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Luis E Arroyo-Mora
- Department of Forensic and Investigative Science, West Virginia University, 1600 University Avenue. Morgantown West Virginia 26505
| | - Anthony P DeCaprio
- Department of Chemistry and Biochemistry, International Forensic Research Institute (IFRI), Florida International University, Miami, Florida 33199, USA
| | - Dionysios D Dionysiou
- Environmental Engineering and Science Program, Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, Ohio 45221, USA
| | - Kevin E O'Shea
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Virender K Sharma
- Department of Environmental and Occupational Health, School of Rural Public Health, Texas A&M University, Texas 77843, USA.
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9
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Park W, Filatov (Gulak) M, Sadiq S, Gerasimov I, Lee S, Joo T, Choi CH. A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate. J Phys Chem Lett 2022; 13:7072-7080. [PMID: 35900137 PMCID: PMC9358713 DOI: 10.1021/acs.jpclett.2c01694] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/11/2022] [Indexed: 05/28/2023]
Abstract
It is well-known that photolysis of pyrimidine nucleobases, such as uracil, in an aqueous environment results in the formation of hydrate as one of the main products. Although several hypotheses regarding photohydration have been proposed in the past, e.g., the zwitterionic and "hot" ground-state mechanisms, its detailed mechanism remains elusive. Here, theoretical nonadiabatic simulations of the uracil photodynamics reveal the formation of a highly energetic but kinetically stable intermediate that features a half-chair puckered pyrimidine ring and a strongly twisted intracyclic double bond. The existence and the kinetic stability of the intermediate are confirmed by a variety of computational chemistry methods. According to the simulations, the unusual intermediate is mainly formed almost immediately (∼50-200 fs) upon photoabsorption and survives long enough to engage in a hydration reaction with a neighboring water. A plausible mechanism of uracil photohydration is proposed on the basis of the modeling of nucleophilic insertion of water into the twisted double bond of the intermediate.
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Affiliation(s)
- Woojin Park
- Department
of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | | | - Saima Sadiq
- Department
of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Igor Gerasimov
- Department
of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Seunghoon Lee
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Taiha Joo
- Department
of Chemistry, Pohang University of Science
and Technology (POSTECH), Pohang 37673, South Korea
| | - Cheol Ho Choi
- Department
of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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10
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Tashiro R, Sugiyama H. Photoreaction of DNA Containing 5-Halouracil and its Products. Photochem Photobiol 2022; 98:532-545. [PMID: 34543451 PMCID: PMC9197447 DOI: 10.1111/php.13521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/13/2021] [Indexed: 11/30/2022]
Abstract
5-Halouracil, which is a DNA base analog in which the methyl group at the C5 position of thymine is replaced with a halogen atom, has been used in studies of DNA damage. In DNA strands, the uracil radical generated from 5-halouracil causes DNA damage via a hydrogen-abstraction reaction. We analyzed the photoreaction of 5-halouracil in various DNA structures and revealed that the reaction is DNA structure-dependent. In this review, we summarize the results of the analysis of the reactivity of 5-halouracil in various DNA local structures. Among the 5-halouracil molecules, 5-bromouracil has been used as a probe in the analysis of photoinduced electron transfer through DNA. The analysis of groove-binder/DNA and protein/DNA complexes using a 5-bromouracil-based electron transfer system is also described.
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Affiliation(s)
- Ryu Tashiro
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki-Cyo, Suzuka, Mie, 513-8670, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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11
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Chan RCT, Ma C, Wong AKW, Chan CTL, Chow JCL, Kwok WM. Dual Time-Scale Proton Transfer and High-Energy, Long-Lived Excitons Unveiled by Broadband Ultrafast Time-Resolved Fluorescence in Adenine-Uracil RNA Duplexes. J Phys Chem Lett 2022; 13:302-311. [PMID: 34978832 DOI: 10.1021/acs.jpclett.1c03553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In contrast to the immense amount of research on electronically excited DNA, surprisingly little has been done about the excited states of RNA. Herein, we demonstrate an ultrafast broadband time-resolved fluorescence and fluorescence anisotropy study to probe directly the intrinsic fluorescence and overall dynamics of the fluorescence from a homopolymeric adenine·uracil RNA duplex adopting the A-form structure. The results unveiled complex deactivation through distinctive multichannels mediated by states of varied energy, a character of charge transfer, and a lifetime from sub-picosecond to nanoseconds. In particular, we observed an unprecedented kinetic isotopic effect and participation of unusual proton transfer from states in two discrete energies and time domains. We also identified a high-energy nanosecond emission that we attributed to its fluorescence anisotropy to long-lived weakly emissive excitons not reported in DNA. These distinguishing features originate from the stacking, pairing, and local hydration environment specific to the A-form conformation of the adenine·uracil double helix.
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Affiliation(s)
- Ruth Chau-Ting Chan
- College of Chemistry and Environmental Engineering, Shenzhen University, 518071, Shenzhen, Guangdong, P. R. China
| | - Chensheng Ma
- College of Chemistry and Environmental Engineering, Shenzhen University, 518071, Shenzhen, Guangdong, P. R. China
| | - Allen Ka-Wa Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, P. R. China
| | - Chris Tsz-Leung Chan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, P. R. China
| | - Joshua Chiu-Lok Chow
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, P. R. China
| | - Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, P. R. China
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12
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Skotnicki K, Janik I, Sadowska K, Leszczynska G, Bobrowski K. Radiation-Induced Oxidation Reactions of 2-Selenouracil in Aqueous Solutions: Comparison with Sulfur Analog of Uracil. Molecules 2021; 27:molecules27010133. [PMID: 35011366 PMCID: PMC8746332 DOI: 10.3390/molecules27010133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/29/2022] Open
Abstract
One-electron oxidation of 2-selenouracil (2-SeU) by hydroxyl (●OH) and azide (●N3) radicals leads to various primary reactive intermediates. Their optical absorption spectra and kinetic characteristics were studied by pulse radiolysis with UV-vis spectrophotometric and conductivity detection and by the density functional theory (DFT) method. The transient absorption spectra recorded in the reactions of ●OH with 2-SeU are dominated by an absorption band with an λmax = 440 nm, the intensity of which depends on the concentration of 2-SeU and pH. Based on the combination of conductometric and DFT studies, the transient absorption band observed both at low and high concentrations of 2-SeU was assigned to the dimeric 2c-3e Se-Se-bonded radical in neutral form (2●). The dimeric radical (2●) is formed in the reaction of a selenyl-type radical (6●) with 2-SeU, and both radicals are in equilibrium with Keq = 1.3 × 104 M−1 at pH 4 (below the pKa of 2-SeU). Similar equilibrium with Keq = 4.4 × 103 M−1 was determined for pH 10 (above the pKa of 2-SeU), which admittedly involves the same radical (6●) but with a dimeric 2c-3e Se-Se bonded radical in anionic form (2●−). In turn, at the lowest concentration of 2-SeU (0.05 mM) and pH 10, the transient absorption spectrum is dominated by an absorption band with an λmax = 390 nm, which was assigned to the ●OH adduct to the double bond at C5 carbon atom (3●) based on DFT calculations. Similar spectral and kinetic features were also observed during the ●N3-induced oxidation of 2-SeU. In principle, our results mostly revealed similarities in one-electron oxidation pathways of 2-SeU and 2-thiouracil (2-TU). The major difference concerns the stability of dimeric radicals with a 2c-3e chalcogen-chalcogen bond in favor of 2-SeU.
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Affiliation(s)
- Konrad Skotnicki
- Centre of Radiation Research and Technology, Institute of Nuclear Chemistry and Technology, 03-195 Warsaw, Poland;
- Correspondence: (K.S.); (I.J.); Tel.: +48-22-504-1292 (K.S.)
| | - Ireneusz Janik
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
- Correspondence: (K.S.); (I.J.); Tel.: +48-22-504-1292 (K.S.)
| | - Klaudia Sadowska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland; (K.S.); (G.L.)
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland; (K.S.); (G.L.)
| | - Krzysztof Bobrowski
- Centre of Radiation Research and Technology, Institute of Nuclear Chemistry and Technology, 03-195 Warsaw, Poland;
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13
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El-Kalyoubi S, Agili F, Zordok WA, El-Sayed ASA. Synthesis, In Silico Prediction and In Vitro Evaluation of Antimicrobial Activity, DFT Calculation and Theoretical Investigation of Novel Xanthines and Uracil Containing Imidazolone Derivatives. Int J Mol Sci 2021; 22:10979. [PMID: 34681643 PMCID: PMC8539769 DOI: 10.3390/ijms222010979] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 01/08/2023] Open
Abstract
Novel xanthine and imidazolone derivatives were synthesized based on oxazolone derivatives 2a-c as a key intermediate. The corresponding xanthine 3-5 and imidazolone derivatives 6-13 were obtained via reaction of oxazolone derivative 2a-c with 5,6-diaminouracils 1a-e under various conditions. Xanthine compounds 3-5 were obtained by cyclocondensation of 5,6-diaminouracils 1a-c with different oxazolones in glacial acetic acid. Moreover, 5,6-diaminouracils 1a-e were reacted with oxazolones 2a-c in presence of drops of acetic acid under fused condition yielding the imidazolone derivatives 6-13. Furthermore, Schiff base of compounds 14-16 were obtained by condensing 5,6-diaminouracils 1a,b,e with 4-dimethylaminobenzaldehyde in acetic acid. The structural identity of the resulting compounds was resolved by IR, 1H-, 13C-NMR and Mass spectral analyses. The novel synthesized compounds were screened for their antifungal and antibacterial activities. Compounds 3, 6, 13 and 16 displayed the highest activity against Escherichia coli as revealed from the IC50 values (1.8-1.9 µg/mL). The compound 16 displayed a significant antifungal activity against Candia albicans (0.82 µg/mL), Aspergillus flavus (1.2 µg/mL) comparing to authentic antibiotics. From the TEM microgram, the compounds 3, 12, 13 and 16 exhibited a strong deformation to the cellular entities, by interfering with the cell membrane components, causing cytosol leakage, cellular shrinkage and irregularity to the cell shape. In addition, docking study for the most promising antimicrobial tested compounds depicted high binding affinity against acyl carrier protein domain from a fungal type I polyketide synthase (ACP), and Baumannii penicillin- binding protein (PBP). Moreover, compound 12 showed high drug- likeness, and excellent pharmacokinetics, which needs to be in focus for further antimicrobial drug development. The most promising antimicrobial compounds underwent theoretical investigation using DFT calculation.
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Affiliation(s)
- Samar El-Kalyoubi
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr City, Cairo 11651, Egypt
| | - Fatimah Agili
- Chemistry Department, Faculty of Science (Female Section), Jazan University, Jazan 82621, Saudi Arabia;
| | - Wael A. Zordok
- Department of Chemistry, Faculty of Science, Zagazig University, Zagazig 44519, Egypt;
| | - Ashraf S. A. El-Sayed
- Enzymology and Fungal Biotechnology, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt;
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14
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Benito M, Roselló Y, Barceló-Oliver M, Frontera A, Molins E. Uracil Derivatives for Halogen-Bonded Cocrystals. Int J Mol Sci 2021; 22:ijms221910663. [PMID: 34639004 PMCID: PMC8508742 DOI: 10.3390/ijms221910663] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 11/17/2022] Open
Abstract
Among non-covalent interactions, halogen bonding is emerging as a new powerful tool for supramolecular self-assembly. Here, along with a green and effective method, we report three new halogen-bonded cocrystals containing uracil derivatives and 1,2,4,5-tetrafluoro-3,6-diiodobenzene as X-bond donor coformer. These multicomponent solids were prepared both by solvent-drop grinding and solution methods and further characterized by powder and single-crystal X-ray diffraction, Fourier-transformed infrared spectroscopy, and thermal methods (TGA-DSC). In order to study the relative importance of hydrogen versus halogen bonds in the crystal packing, computational methods were applied.
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Affiliation(s)
- Mónica Benito
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
- Correspondence: (M.B.); (A.F.); (E.M.)
| | - Yannick Roselló
- Departament de Química, Universitat de les Illes Balears, Ctra. Valldemosa km 7.5, 07122 Palma de Mallorca, Spain; (Y.R.); (M.B.-O.)
| | - Miquel Barceló-Oliver
- Departament de Química, Universitat de les Illes Balears, Ctra. Valldemosa km 7.5, 07122 Palma de Mallorca, Spain; (Y.R.); (M.B.-O.)
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Ctra. Valldemosa km 7.5, 07122 Palma de Mallorca, Spain; (Y.R.); (M.B.-O.)
- Correspondence: (M.B.); (A.F.); (E.M.)
| | - Elies Molins
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
- Correspondence: (M.B.); (A.F.); (E.M.)
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15
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Valverde D, de Araújo AVS, Borin AC. Photophysical Deactivation Mechanisms of the Pyrimidine Analogue 1-Cyclohexyluracil. Molecules 2021; 26:5191. [PMID: 34500625 PMCID: PMC8434193 DOI: 10.3390/molecules26175191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
The photophysical relaxation mechanisms of 1-cyclohexyluracil, in vacuum and water, were investigated by employing the Multi-State CASPT2 (MS-CASPT2, Multi-State Complete Active-Space Second-Order Perturbation Theory) quantum chemical method and Dunning's cc-pVDZ basis sets. In both environments, our results suggest that the primary photophysical event is the population of the S11(ππ*) bright state. Afterwards, two likely deactivation pathways can take place, which is sustained by linear interpolation in internal coordinates defined via Z-Matrix scans connecting the most important characteristic points. The first one (Route 1) is the same relaxation mechanism observed for uracil, its canonical analogue, i.e., internal conversion to the ground state through an ethylenic-like conical intersection. The other route (Route 2) is the direct population transfer from the S11(ππ*) bright state to the T23(nπ*) triplet state via an intersystem crossing process involving the (S11(ππ*)/T23(nπ*))STCP singlet-triplet crossing point. As the spin-orbit coupling is not too large in either environment, we propose that most of the electronic population initially on the S11(ππ*) state returns to the ground following the same ultrafast deactivation mechanism observed in uracil (Route 1), while a smaller percentage goes to the triplet manifold. The presence of a minimum on the S11(ππ*) potential energy hypersurface in water can help to understand why experimentally it is noticed suppression of the triplet states population in polar protic solvent.
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Affiliation(s)
- Danillo Valverde
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil;
| | | | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil;
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16
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Shang Y, Wu C, Gao Q, Liu C, Li L, Zhang X, Cheng HG, Liu S, Zhou Q. Diversity-oriented functionalization of 2-pyridones and uracils. Nat Commun 2021; 12:2988. [PMID: 34016986 PMCID: PMC8137914 DOI: 10.1038/s41467-021-23058-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/09/2021] [Indexed: 11/28/2022] Open
Abstract
Heterocycles 2-pyridone and uracil are privileged pharmacophores. Diversity-oriented synthesis of their derivatives is in urgent need in medicinal chemistry. Herein, we report a palladium/norbornene cooperative catalysis enabled dual-functionalization of iodinated 2-pyridones and uracils. The success of this research depends on the use of two unique norbornene derivatives as the mediator. Readily available alkyl halides/tosylates and aryl bromides are utilized as ortho-alkylating and -arylating reagents, respectively. Widely accessible ipso-terminating reagents, including H/DCO2Na, boronic acid/ester, terminal alkene and alkyne are compatible with this protocol. Thus, a large number of valuable 2-pyridone derivatives, including deuterium/CD3-labeled 2-pyridones, bicyclic 2-pyridones, 2-pyridone-fenofibrate conjugate, axially chiral 2-pyridone (97% ee), as well as uracil and thymine derivatives, can be quickly prepared in a predictable manner (79 examples reported), which will be very useful in new drug discovery.
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Affiliation(s)
- Yong Shang
- Sauvage Center for Molecular Sciences, Engineering Research Center of Organosilicon Compounds & Materials (Ministry of Education), College of Chemistry and Molecular Sciences, and The Institute for Advanced Studies, Wuhan, China
| | - Chenggui Wu
- Sauvage Center for Molecular Sciences, Engineering Research Center of Organosilicon Compounds & Materials (Ministry of Education), College of Chemistry and Molecular Sciences, and The Institute for Advanced Studies, Wuhan, China
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Qianwen Gao
- Sauvage Center for Molecular Sciences, Engineering Research Center of Organosilicon Compounds & Materials (Ministry of Education), College of Chemistry and Molecular Sciences, and The Institute for Advanced Studies, Wuhan, China
| | - Chang Liu
- Sauvage Center for Molecular Sciences, Engineering Research Center of Organosilicon Compounds & Materials (Ministry of Education), College of Chemistry and Molecular Sciences, and The Institute for Advanced Studies, Wuhan, China
| | - Lisha Li
- Sauvage Center for Molecular Sciences, Engineering Research Center of Organosilicon Compounds & Materials (Ministry of Education), College of Chemistry and Molecular Sciences, and The Institute for Advanced Studies, Wuhan, China
| | - Xinping Zhang
- Sauvage Center for Molecular Sciences, Engineering Research Center of Organosilicon Compounds & Materials (Ministry of Education), College of Chemistry and Molecular Sciences, and The Institute for Advanced Studies, Wuhan, China
| | - Hong-Gang Cheng
- Sauvage Center for Molecular Sciences, Engineering Research Center of Organosilicon Compounds & Materials (Ministry of Education), College of Chemistry and Molecular Sciences, and The Institute for Advanced Studies, Wuhan, China
| | - Shanshan Liu
- Sauvage Center for Molecular Sciences, Engineering Research Center of Organosilicon Compounds & Materials (Ministry of Education), College of Chemistry and Molecular Sciences, and The Institute for Advanced Studies, Wuhan, China
| | - Qianghui Zhou
- Sauvage Center for Molecular Sciences, Engineering Research Center of Organosilicon Compounds & Materials (Ministry of Education), College of Chemistry and Molecular Sciences, and The Institute for Advanced Studies, Wuhan, China.
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17
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Petera L, Mrazikova K, Nejdl L, Zemankova K, Vaculovicova M, Pastorek A, Civis S, Kubelik P, Heays A, Cassone G, Sponer J, Ferus M, Sponer J. Prebiotic Route to Thymine from Formamide-A Combined Experimental-Theoretical Study. Molecules 2021; 26:molecules26082248. [PMID: 33924594 PMCID: PMC8069957 DOI: 10.3390/molecules26082248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 12/02/2022] Open
Abstract
Synthesis of RNA nucleobases from formamide is one of the recurring topics of prebiotic chemistry research. Earlier reports suggest that thymine, the substitute for uracil in DNA, may also be synthesized from formamide in the presence of catalysts enabling conversion of formamide to formaldehyde. In the current paper, we show that to a lesser extent conversion of uracil to thymine may occur even in the absence of catalysts. This is enabled by the presence of formic acid in the reaction mixture that forms as the hydrolysis product of formamide. Under the reaction conditions of our study, the disproportionation of formic acid may produce formaldehyde that hydroxymethylates uracil in the first step of the conversion process. The experiments are supplemented by quantum chemical modeling of the reaction pathway, supporting the plausibility of the mechanism suggested by Saladino and coworkers.
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Affiliation(s)
- Lukáš Petera
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
| | - Klaudia Mrazikova
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ 61265 Brno, Czech Republic; (K.M.); (J.S.)
| | - Lukas Nejdl
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, CZ 61300 Brno, Czech Republic; (K.Z.); (M.V.)
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ 61200 Brno, Czech Republic
- Correspondence: (L.N.); (M.F.); (J.S.)
| | - Kristyna Zemankova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, CZ 61300 Brno, Czech Republic; (K.Z.); (M.V.)
| | - Marketa Vaculovicova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, CZ 61300 Brno, Czech Republic; (K.Z.); (M.V.)
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ 61200 Brno, Czech Republic
| | - Adam Pastorek
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
| | - Svatopluk Civis
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
| | - Petr Kubelik
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
| | - Alan Heays
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
| | - Giuseppe Cassone
- Institute for Chemical-Physical Processes, Italian National Research Council (IPCF-CNR), Viale Ferdinando Stagno d’Alcontres 37, 98158 Messina, Italy;
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ 61265 Brno, Czech Republic; (K.M.); (J.S.)
| | - Martin Ferus
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, CZ 18223 Prague 8, Czech Republic; (L.P.); (A.P.); (S.C.); (P.K.); (A.H.)
- Correspondence: (L.N.); (M.F.); (J.S.)
| | - Judit Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ 61265 Brno, Czech Republic; (K.M.); (J.S.)
- Correspondence: (L.N.); (M.F.); (J.S.)
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18
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Reddy NN, Hung SJ, Swamy MK, Sanjeev A, Rao VS, Rohini R, Raju AK, Bhaskar K, Hu A, Reddy PM. Synthesis and Rational Design of New Appended 1,2,3-Triazole-uracil Ensembles as Promising Anti-Tumor Agents via In Silico VEGFR-2 Transferase Inhibition. Molecules 2021; 26:1952. [PMID: 33808444 PMCID: PMC8037033 DOI: 10.3390/molecules26071952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 11/18/2022] Open
Abstract
Angiogenesis inhibition is a key step towards the designing of new chemotherapeutic agents. In a view to preparing new molecular entities for cancer treatment, eighteen 1,2,3-triazole-uracil ensembles 5a-r were designed and synthesized via the click reaction. The ligands were well characterized using 1H-, 13C-NMR, elemental analysis and ESI-mass spectrometry. The in silico binding propinquities of the ligands were studied sequentially in the active region of VEGFR-2 using the Molegro virtual docker. All the compounds produced remarkable interactions and potentially inhibitory ligands against VEGFR-2 were obtained with high negative binding energies. Drug-likeness was assessed from the ADME properties. Cytotoxicity of the test compounds was measured against HeLa and HUH-7 tumor cells and NIH/3T3 normal cells by MTT assay. Compound 5h showed higher growth inhibition activity than the positive control, 5-fluorouracil (5-FU), against both HeLa and HUH-7 cells with IC50 values of 4.5 and 7.7 μM respectively. Interestingly, the compounds 5a-r did not show any cytotoxicity towards the normal cell lines. The results advance the position of substituted triazoles in the area of drug design with no ambiguity.
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Affiliation(s)
- Nadipolla Naresh Reddy
- Department of Chemistry, Osmania University, Hyderabad, Telangana 500007, India; (N.N.R.); (M.K.S.); (A.S.); (V.S.R.); (R.R.); (K.B.)
| | - Sung-Jen Hung
- Department of Dermatology, Buddhist Tzu-Chi General Hospital, Hualien 97002, Taiwan;
- Institute of Medical Sciences, Tzu-Chi University, Hualien 97002, Taiwan
| | - Merugu Kumara Swamy
- Department of Chemistry, Osmania University, Hyderabad, Telangana 500007, India; (N.N.R.); (M.K.S.); (A.S.); (V.S.R.); (R.R.); (K.B.)
| | - Ananthula Sanjeev
- Department of Chemistry, Osmania University, Hyderabad, Telangana 500007, India; (N.N.R.); (M.K.S.); (A.S.); (V.S.R.); (R.R.); (K.B.)
| | - Vankadari Srinivasa Rao
- Department of Chemistry, Osmania University, Hyderabad, Telangana 500007, India; (N.N.R.); (M.K.S.); (A.S.); (V.S.R.); (R.R.); (K.B.)
| | - Rondla Rohini
- Department of Chemistry, Osmania University, Hyderabad, Telangana 500007, India; (N.N.R.); (M.K.S.); (A.S.); (V.S.R.); (R.R.); (K.B.)
| | - Atcha Krishnam Raju
- Department of Chemistry, Nizam College, Osmania University, Hyderabad 500001, India;
| | - Kuthati Bhaskar
- Department of Chemistry, Osmania University, Hyderabad, Telangana 500007, India; (N.N.R.); (M.K.S.); (A.S.); (V.S.R.); (R.R.); (K.B.)
| | - Anren Hu
- Institute of Medical Sciences, Tzu-Chi University, Hualien 97002, Taiwan
- Department of Laboratory Medicine and Biotechnology, College of Medicine, Tzu-Chi University, Hualien 97004, Taiwan
| | - Puchakayala Muralidhar Reddy
- Department of Chemistry, Osmania University, Hyderabad, Telangana 500007, India; (N.N.R.); (M.K.S.); (A.S.); (V.S.R.); (R.R.); (K.B.)
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19
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Green JA, Jouybari MY, Aranda D, Improta R, Santoro F. Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases. Molecules 2021; 26:1743. [PMID: 33804640 PMCID: PMC8003674 DOI: 10.3390/molecules26061743] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 11/16/2022] Open
Abstract
We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2-3 bright states and all the close by dark states, for a total of 6-9 states, and including all the normal coordinates. We adopted two different functionals, CAM-B3LYP and PBE0, and tested the effect of the basis set. Computed spectra are in good agreement with the available experimental data, remarkably improving over pure electronic computations, but also with respect to vibronic spectra obtained neglecting inter-state couplings. Our QD simulations indicate an effective population transfer from the lowest energy bright excited states to the close-lying dark excited states for uracil, thymine and adenine. Dynamics from higher-energy states show an ultrafast depopulation toward the more stable ones. The proposed protocol is sufficiently general and automatic to promise to become useful for widespread applications.
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Affiliation(s)
- James A. Green
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy;
| | - Martha Yaghoubi Jouybari
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| | - Daniel Aranda
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| | - Roberto Improta
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy;
| | - Fabrizio Santoro
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
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20
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Gürel HH, Salmankurt B. Quantum Simulation of the Silicene and Germanene for Sensing and Sequencing of DNA/RNA Nucleobases. Biosensors (Basel) 2021; 11:59. [PMID: 33668284 PMCID: PMC7996300 DOI: 10.3390/bios11030059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
Over the last decade, we have been witnessing the rise of two-dimensional (2D) materials. Several 2D materials with outstanding properties have been theoretically predicted and experimentally synthesized. 2D materials are good candidates for sensing and detecting various biomolecules because of their extraordinary properties, such as a high surface-to-volume ratio. Silicene and germanene are the monolayer honeycomb structures of silicon and germanium, respectively. Quantum simulations have been very effective in understanding the interaction mechanism of 2D materials and biomolecules and may play an important role in the development of effective and reliable biosensors. This article focuses on understanding the interaction of DNA/RNA nucleobases with silicene and germanane monolayers and obtaining the possibility of using silicene and germanane monolayers as a biosensor for DNA/RNA nucleobases' sequencing using the first principle of Density Functional Theory (DFT) calculations with van der Waals (vdW) correction and nonequilibrium Green's function method. Guanine (G), Cytosine (C), Adenine (A), Thymine (T), and Uracil (U) were examined as the analytes. The strength of adsorption between the DNA/RNA nucleobases and silicene and germanane is G > C > A > T > U. Moreover, our recent work on the investigation of Au- and Li-decorated silicene and germanane for detection of DNA/RNA nucleobases is presented. Our results show that it is possible to get remarkable changes in transmittance due to the adsorption of nucleobases, especially for G, A, and C. These results indicate that silicene and germanene are both good candidates for the applications in fast sequencing devices for DNA/RNA nucleobases. Additionally, our present results have the potential to give insight into experimental studies and can be valuable for advancements in biosensing and nanobiotechnology.
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Affiliation(s)
- Hikmet Hakan Gürel
- Information Systems Engineering Department, Technology Faculty, Umuttepe Campus, Kocaeli University, Kocaeli 41001, Turkey;
| | - Bahadır Salmankurt
- Information Systems Engineering Department, Technology Faculty, Umuttepe Campus, Kocaeli University, Kocaeli 41001, Turkey;
- Department of Physics, Art and Science Faculty, Esentepe Campus, Sakarya University, Sakarya 54187, Turkey
- Remote Education Center, Sakarya University of Applied Sciences, Sakarya 54187, Turkey
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Abstract
In a recent publication, Eleftheriou et al. proposed that inhibitors of dipeptidyl peptidase‐4 (DPP‐4) are functional inhibitors of the main protease (Mpro) of SARS‐CoV‐2. Their predictions prompted the authors to suggest linagliptin, a DPP‐4 inhibitor and approved anti‐diabetes drug, as a repurposed drug candidate against the ongoing COVID‐19 pandemic. We used an enzymatic assay measuring the inhibition of Mpro catalytic activity in the presence of four different commercially available gliptins (linagliptin, sitagliptin, alogliptin and saxagliptin) and several structural analogues of linagliptin to study the binding of DPP‐4 inhibitors to Mpro and their functional activity. We show here that DPP‐4 inhibitors like linagliptin, other gliptins and structural analogues are inactive against Mpro.
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Affiliation(s)
- Herbert Nar
- Boehringer-Ingelheim Pharma, GmbH & Co. KGBirkendorferstr. 6588397 BiberachGermany
| | - Gisela Schnapp
- Boehringer-Ingelheim Pharma, GmbH & Co. KGBirkendorferstr. 6588397 BiberachGermany
| | - Oliver Hucke
- Boehringer-Ingelheim Pharma, GmbH & Co. KGBirkendorferstr. 6588397 BiberachGermany
| | | | - Thomas Klein
- Boehringer-Ingelheim Pharma, GmbH & Co. KGBirkendorferstr. 6588397 BiberachGermany
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Pullen S, Hegmans A, Hiller WG, Platzek A, Freisinger E, Lippert B. On the Heterogeneous Nature of Cisplatin-1-Methyluracil Complexes: Coexistence of Different Aggregation Modes and Partial Loss of NH 3 Ligands as Likely Explanation. ChemistryOpen 2021; 10:28-45. [PMID: 33448132 PMCID: PMC7809254 DOI: 10.1002/open.202000317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/10/2020] [Indexed: 11/22/2022] Open
Abstract
The conversion of the 1 : 1-complex of Cisplatin with 1-methyluracil (1MeUH), cis-[Pt(NH3 )2 (1MeU-N3)Cl] (1 a) to the aqua species cis-[Pt(NH3 )2 (1MeU-N3)(OH2 )]+ (1 b), achieved by reaction of 1 a with AgNO3 in water, affords a mixture of compounds, the composition of which strongly depends on sample history. The complexity stems from variations in condensation patterns and partial loss of NH3 ligands. In dilute aqueous solution, 1 a, and dinuclear compounds cis-[(NH3 )2 (1MeU-N3)Pt(μ-OH)Pt(1MeU-N3)(NH3 )2 ]+ (3) as well as head-tail cis-[Pt2 (NH3 )4 (μ-1MeU-N3,O4)2 ]2+ (4) represent the major components. In addition, there are numerous other species present in minor quantities, which differ in metal nuclearity, stoichiometry, stereoisomerism, and Pt oxidation state, as revealed by a combination of 1 H NMR and ESI-MS spectroscopy. Their composition appears not to be the consequence of a unique and repeating coordination pattern of the 1MeU ligand in oligomers but rather the coexistence of distinctly different condensation patterns, which include μ-OH, μ-1MeU, and μ-NH2 bridging and combinations thereof. Consequently, the products obtained should, in total, be defined as a heterogeneous mixture rather than a mixture of oligomers of different sizes. In addition, a N2 complex, [Pt(NH3 )(1MeU)(N2 )]+ appears to be formed in gas phase during the ESI-MS experiment. In the presence of Na+ ions, multimers n of 1 a with n=2, 3, 4 are formed that represent analogues of non-metalated uracil quartets found in tetrastranded RNA.
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Affiliation(s)
- Sonja Pullen
- Fakultät Chemie und Chemische Biologie (CCB)Technische Universität DortmundOtto-Hahn-Str. 644221DortmundGermany
| | - Alexander Hegmans
- Fakultät Chemie und Chemische Biologie (CCB)Technische Universität DortmundOtto-Hahn-Str. 644221DortmundGermany
| | - Wolf G. Hiller
- Fakultät Chemie und Chemische Biologie (CCB)Technische Universität DortmundOtto-Hahn-Str. 644221DortmundGermany
| | - André Platzek
- Fakultät Chemie und Chemische Biologie (CCB)Technische Universität DortmundOtto-Hahn-Str. 644221DortmundGermany
| | - Eva Freisinger
- Fakultät Chemie und Chemische Biologie (CCB)Technische Universität DortmundOtto-Hahn-Str. 644221DortmundGermany
- Department of ChemistryUniversity of ZurichWinterthurerstrasse 1908057ZurichSwitzerland
| | - Bernhard Lippert
- Fakultät Chemie und Chemische Biologie (CCB)Technische Universität DortmundOtto-Hahn-Str. 644221DortmundGermany
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23
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Gollapudi SK, Yu M, Gan QF, Nag S. Synthetic thick filaments: A new avenue for better understanding the myosin super-relaxed state in healthy, diseased, and mavacamten-treated cardiac systems. J Biol Chem 2021; 296:100114. [PMID: 33234590 PMCID: PMC7948491 DOI: 10.1074/jbc.ra120.016506] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
A hallmark feature of myosin-II is that it can spontaneously self-assemble into bipolar synthetic thick filaments (STFs) in low-ionic-strength buffers, thereby serving as a reconstituted in vitro model for muscle thick filaments. Although these STFs have been extensively used for structural characterization, their functional evaluation has been limited. In this report, we show that myosins in STFs mirror the more electrostatic and cooperative interactions that underlie the energy-sparing super-relaxed (SRX) state, which are not seen using shorter myosin subfragments, heavy meromyosin (HMM) and myosin subfragment 1 (S1). Using these STFs, we show several pathophysiological insults in hypertrophic cardiomyopathy, including the R403Q myosin mutation, phosphorylation of myosin light chains, and an increased ADP:ATP ratio, destabilize the SRX population. Furthermore, WT myosin containing STFs, but not S1, HMM, or STFs-containing R403Q myosin, recapitulated the ADP-induced destabilization of the SRX state. Studies involving a clinical-stage small-molecule inhibitor, mavacamten, showed that it is more effective in not only increasing myosin SRX population in STFs than in S1 or HMM but also in increasing myosin SRX population equally well in STFs made of healthy and disease-causing R403Q myosin. Importantly, we also found that pathophysiological perturbations such as elevated ADP concentration weakens mavacamten's ability to increase the myosin SRX population, suggesting that mavacamten-bound myosin heads are not permanently protected in the SRX state but can be recruited into action. These findings collectively emphasize that STFs serve as a valuable tool to provide novel insights into the myosin SRX state in healthy, diseased, and therapeutic conditions.
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Affiliation(s)
| | - Ming Yu
- Department of Biology, MyoKardia, Inc., Brisbane, California, USA
| | - Qing-Fen Gan
- Department of Biology, MyoKardia, Inc., Brisbane, California, USA
| | - Suman Nag
- Department of Biology, MyoKardia, Inc., Brisbane, California, USA.
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24
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Abstract
C-Analogues of the canonical N-nucleosides have considerable importance in medicinal chemistry and are promising building blocks of xenobiotic nucleic acids (XNA) in synthetic biology. Although well established for synthesis of N-nucleosides, biocatalytic methods are lacking in C-nucleoside synthetic chemistry. Here, we identify pseudouridine monophosphate C-glycosidase for selective 5-β-C-glycosylation of uracil and derivatives thereof from pentose 5-phosphate (D-ribose, 2-deoxy-D-ribose, D-arabinose, D-xylose) substrates. Substrate requirements of the enzymatic reaction are consistent with a Mannich-like addition between the pyrimidine nucleobase and the iminium intermediate of enzyme (Lys166) and open-chain pentose 5-phosphate. β-Elimination of the lysine and stereoselective ring closure give the product. We demonstrate phosphorylation-glycosylation cascade reactions for efficient, one-pot synthesis of C-nucleoside phosphates (yield: 33 - 94%) from unprotected sugar and nucleobase. We show incorporation of the enzymatically synthesized C-nucleotide triphosphates into nucleic acids by RNA polymerase. Collectively, these findings implement biocatalytic methodology for C-nucleotide synthesis which can facilitate XNA engineering for synthetic biology applications.
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Affiliation(s)
- Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010, Graz, Austria
- Austrian Centre of Industrial Biotechnology (acib), Petersgasse 14, 8010, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010, Graz, Austria.
- Austrian Centre of Industrial Biotechnology (acib), Petersgasse 14, 8010, Graz, Austria.
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25
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Rouquette L, Stalport F, Cottin H, Colas C, Georgelin T, Chaouche-Mechidal N, Lasne J, Mahfouf S, Raulin F, Selliez L, Szopa C, Coll P. Dimerization of Uracil in a Simulated Mars-like UV Radiation Environment. Astrobiology 2020; 20:1363-1376. [PMID: 33179968 DOI: 10.1089/ast.2019.2157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The search for organic molecules at the surface of Mars is a key objective in astrobiology, given that many organic compounds are possible biosignatures and their presence is of interest with regard to the habitability of Mars. Current environmental conditions at the martian surface are harsh and affect the stability of organic molecules. For this reason, and because current and future Mars rovers collect samples from the upper surface layer, it is important to assess the fate of organic molecules under the conditions at the martian surface. Here, we present an experimental study of the evolution of uracil when exposed to UV radiation, pressure, and temperature conditions representative of the surface of Mars. Uracil was selected because it is a nucleobase that composes RNA, and it has been detected in interplanetary bodies that could be the exogenous source of this molecule by meteoritic delivery to the surface of Mars. Our results show that the experimental quantum efficiency of photodecomposition of uracil is 0.16 ± 0.14 molecule/photon. Although these results suggest that uracil is quickly photodegraded when directly exposed to UV light on Mars, such exposure produces dimers that are more stable over time than the monomer. The identified dimers could be targets of interest for current and future Mars space missions.
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Affiliation(s)
- Laura Rouquette
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université de Paris, Institut Pierre Simon Laplace, Creteil Cedex, France
| | - Fabien Stalport
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université de Paris, Institut Pierre Simon Laplace, Creteil Cedex, France
| | - Hervé Cottin
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université de Paris, Institut Pierre Simon Laplace, Creteil Cedex, France
| | - Cyril Colas
- Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans, UMR CNRS 7311, Orléans, France
- Centre de Biophysique Moléculaire (CBM), UPR CNRS 4301, Université d'Orléans, Orléans, France
| | - Thomas Georgelin
- Centre de Biophysique Moléculaire (CBM), UPR CNRS 4301, Université d'Orléans, Orléans, France
- Laboratoire de Réactivité de Surface, UMR CNRS 7197, Sorbonne Université, Paris, France
| | - Naïla Chaouche-Mechidal
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université de Paris, Institut Pierre Simon Laplace, Creteil Cedex, France
| | - Jerome Lasne
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université de Paris, Institut Pierre Simon Laplace, Creteil Cedex, France
| | - Sara Mahfouf
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université de Paris, Institut Pierre Simon Laplace, Creteil Cedex, France
| | - François Raulin
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université de Paris, Institut Pierre Simon Laplace, Creteil Cedex, France
| | - Laura Selliez
- Laboratoire de Physique et Chimie de l'Environnement et de l'Espace (LPC2E), UMR CNRS7328, Université d'Orléans, Orléans Cedex, France
- Laboratoire atmosphères, milieux, observations spatiales, Institut Pierre Simon Laplace, UMR 8190, UVSQ Université Paris-Saclay, Sorbonne Université, CNRS, Guyancourt, France
| | - Cyril Szopa
- Laboratoire atmosphères, milieux, observations spatiales, Institut Pierre Simon Laplace, UMR 8190, UVSQ Université Paris-Saclay, Sorbonne Université, CNRS, Guyancourt, France
- Institut Universitaire de France, Paris, France
| | - Patrice Coll
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université de Paris, Institut Pierre Simon Laplace, Creteil Cedex, France
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26
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Awad W, Meermeier EW, Sandoval-Romero ML, Le Nours J, Worley AH, Null MD, Liu L, McCluskey J, Fairlie DP, Lewinsohn DM, Rossjohn J. Atypical TRAV1-2 - T cell receptor recognition of the antigen-presenting molecule MR1. J Biol Chem 2020; 295:14445-14457. [PMID: 32817339 PMCID: PMC7573270 DOI: 10.1074/jbc.ra120.015292] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Indexed: 12/15/2022] Open
Abstract
MR1 presents vitamin B-related metabolites to mucosal associated invariant T (MAIT) cells, which are characterized, in part, by the TRAV1-2+ αβ T cell receptor (TCR). In addition, a more diverse TRAV1-2- MR1-restricted T cell repertoire exists that can possess altered specificity for MR1 antigens. However, the molecular basis of how such TRAV1-2- TCRs interact with MR1-antigen complexes remains unclear. Here, we describe how a TRAV12-2+ TCR (termed D462-E4) recognizes an MR1-antigen complex. We report the crystal structures of the unliganded D462-E4 TCR and its complex with MR1 presenting the riboflavin-based antigen 5-OP-RU. Here, the TRBV29-1 β-chain of the D462-E4 TCR binds over the F'-pocket of MR1, whereby the complementarity-determining region (CDR) 3β loop surrounded and projected into the F'-pocket. Nevertheless, the CDR3β loop anchored proximal to the MR1 A'-pocket and mediated direct contact with the 5-OP-RU antigen. The D462-E4 TCR footprint on MR1 contrasted that of the TRAV1-2+ and TRAV36+ TCRs' docking topologies on MR1. Accordingly, diverse MR1-restricted T cell repertoire reveals differential docking modalities on MR1, thus providing greater scope for differing antigen specificities.
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MESH Headings
- Amino Acid Sequence
- Antigen Presentation
- Binding Sites
- Crystallography, X-Ray
- Histocompatibility Antigens Class I/chemistry
- Histocompatibility Antigens Class I/genetics
- Histocompatibility Antigens Class I/metabolism
- Humans
- Minor Histocompatibility Antigens/chemistry
- Minor Histocompatibility Antigens/genetics
- Minor Histocompatibility Antigens/metabolism
- Molecular Docking Simulation
- Protein Refolding
- Protein Structure, Tertiary
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Ribitol/analogs & derivatives
- Ribitol/chemistry
- Ribitol/metabolism
- Surface Plasmon Resonance
- T-Lymphocytes/cytology
- T-Lymphocytes/metabolism
- Uracil/analogs & derivatives
- Uracil/chemistry
- Uracil/metabolism
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Affiliation(s)
- Wael Awad
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Erin W Meermeier
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Maria L Sandoval-Romero
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jérôme Le Nours
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Aneta H Worley
- Veterans Affairs Portland Health Care Center, Portland, Oregon, USA
| | - Megan D Null
- Department of Pediatrics, Oregon Health & Science University, Portland, Oregon, USA
| | - Ligong Liu
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Brisbane, Queensland, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - David P Fairlie
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Brisbane, Queensland, Australia
| | - David M Lewinsohn
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, Oregon, USA
- Veterans Affairs Portland Health Care Center, Portland, Oregon, USA
- Department of Pulmonary & Critical Care Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, United Kingdom
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27
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Felicetti S, Fregoni J, Schnappinger T, Reiter S, de Vivie-Riedle R, Feist J. Photoprotecting Uracil by Coupling with Lossy Nanocavities. J Phys Chem Lett 2020; 11:8810-8818. [PMID: 32914984 PMCID: PMC7569670 DOI: 10.1021/acs.jpclett.0c02236] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/11/2020] [Indexed: 05/08/2023]
Abstract
We analyze how the photorelaxation dynamics of a molecule can be controlled by modifying its electromagnetic environment using a nanocavity mode. In particular, we consider the photorelaxation of the RNA nucleobase uracil, which is the natural mechanism to prevent photodamage. In our theoretical work, we identify the operative conditions in which strong coupling with the cavity mode can open an efficient photoprotective channel, resulting in a relaxation dynamics twice as fast as the natural one. We rely on a state-of-the-art chemically detailed molecular model and a non-Hermitian Hamiltonian propagation approach to perform full-quantum simulations of the system dissipative dynamics. By focusing on the photon decay, our analysis unveils the active role played by cavity-induced dissipative processes in modifying chemical reaction rates, in the context of molecular polaritonics. Remarkably, we find that the photorelaxation efficiency is maximized when an optimal trade-off between light-matter coupling strength and photon decay rate is satisfied. This result is in contrast with the common intuition that increasing the quality factor of nanocavities and plasmonic devices improves their performance. Finally, we use a detailed model of a metal nanoparticle to show that the speedup of the uracil relaxation could be observed via coupling with a nanosphere pseudomode, without requiring the implementation of complex nanophotonic structures.
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Affiliation(s)
- Simone Felicetti
- Istituto
di Fotonica e Nanotecnologie, Consiglio
Nazionale delle Ricerche (IFN-CNR), Milano, Italy
- Departamento
de Física Teórica
de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autonoma de Madrid, Madrid, Spain
| | - Jacopo Fregoni
- Dipartimento
di Scienze Chimiche, University of Padova, Padova, Italy
- Dipartimento
di Scienze Fisiche, Informatiche e Matematiche, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Sebastian Reiter
- Department
Chemie, Ludwig-Maximilians-Universität
München, München, Germany
| | | | - Johannes Feist
- Departamento
de Física Teórica
de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autonoma de Madrid, Madrid, Spain
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28
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Semenov VE, Zueva IV, Mukhamedyarov MA, Lushchekina SV, Petukhova EO, Gubaidullina LM, Krylova ES, Saifina LF, Lenina OA, Petrov KA. Novel Acetylcholinesterase Inhibitors Based on Uracil Moiety for Possible Treatment of Alzheimer Disease. Molecules 2020; 25:molecules25184191. [PMID: 32932702 PMCID: PMC7571187 DOI: 10.3390/molecules25184191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/07/2020] [Accepted: 09/10/2020] [Indexed: 12/14/2022] Open
Abstract
In this study, novel derivatives based on 6-methyluracil and condensed uracil were synthesized, namely, 2,4-quinazoline-2,4-dione with ω-(ortho-nitrilebenzylethylamino) alkyl chains at the N atoms of the pyrimidine ring. In this series of synthesized compounds, the polymethylene chains were varied from having tetra- to hexamethylene chains, and secondary NH, tertiary ethylamino, and quaternary ammonium groups were introduced into the chains. The molecular modeling of the compounds indicated that they could function as dual binding site acetylcholinesterase inhibitors, binding to both the peripheral anionic site and active site. The data from in vitro experiments show that the most active compounds exhibit affinity toward acetylcholinesterase within a nanomolar range, with selectivity for acetylcholinesterase over butyrylcholinesterase reaching four orders of magnitude. In vivo biological assays demonstrated the potency of these compounds in the treatment of memory impairment using an animal model of Alzheimer disease.
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Affiliation(s)
- Vyacheslav E. Semenov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Arbuzov str. 8, 420088 Kazan, Russia; (I.V.Z.); (L.M.G.); (E.S.K.); (L.F.S.); (O.A.L.)
- Correspondence: (V.E.S.); (K.A.P.); Tel.: +7-843-279-47-09 (V.E.S.); +7-843-273-93-64 (K.A.P.)
| | - Irina V. Zueva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Arbuzov str. 8, 420088 Kazan, Russia; (I.V.Z.); (L.M.G.); (E.S.K.); (L.F.S.); (O.A.L.)
| | - Marat A. Mukhamedyarov
- Institute of Neuroscience, Kazan State Medical University, 420012 Kazan, Russia; (M.A.M.); (E.O.P.)
| | - Sofya V. Lushchekina
- Emanuel Institute of Biochemical Physics, Kosygina st. 4, 119334 Moscow, Russia;
| | - Elena O. Petukhova
- Institute of Neuroscience, Kazan State Medical University, 420012 Kazan, Russia; (M.A.M.); (E.O.P.)
| | - Lilya M. Gubaidullina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Arbuzov str. 8, 420088 Kazan, Russia; (I.V.Z.); (L.M.G.); (E.S.K.); (L.F.S.); (O.A.L.)
| | - Evgeniya S. Krylova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Arbuzov str. 8, 420088 Kazan, Russia; (I.V.Z.); (L.M.G.); (E.S.K.); (L.F.S.); (O.A.L.)
| | - Lilya F. Saifina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Arbuzov str. 8, 420088 Kazan, Russia; (I.V.Z.); (L.M.G.); (E.S.K.); (L.F.S.); (O.A.L.)
| | - Oksana A. Lenina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Arbuzov str. 8, 420088 Kazan, Russia; (I.V.Z.); (L.M.G.); (E.S.K.); (L.F.S.); (O.A.L.)
| | - Konstantin A. Petrov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, Arbuzov str. 8, 420088 Kazan, Russia; (I.V.Z.); (L.M.G.); (E.S.K.); (L.F.S.); (O.A.L.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlyovskaya str., 18, 420008 Kazan, Russia
- Correspondence: (V.E.S.); (K.A.P.); Tel.: +7-843-279-47-09 (V.E.S.); +7-843-273-93-64 (K.A.P.)
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29
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Cabaj MK, Dominiak PM. Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals. Nucleic Acids Res 2020; 48:8302-8319. [PMID: 32725210 PMCID: PMC7470937 DOI: 10.1093/nar/gkaa629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/10/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022] Open
Abstract
We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar structures. The investigated compounds were either free forms or derivatives of adenine, guanine, hypoxanthine, thymine, uracil and cytosine. We divided our findings into categories including types of pairs, protonation patterns and whether they are formed by free bases or substituted ones. We found base pair types that are exclusive to small molecule crystal structures, some that can be found only in RNA containing crystal structures and many that are native to both environments. With a few exceptions, nucleobase protonation generally followed a standard pattern governed by pKa values. The lengths of hydrogen bonds did not depend on whether the nucleobases forming a base pair were charged or not. The reasons why particular nucleobases formed base pairs in a certain way varied significantly.
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Affiliation(s)
- Małgorzata Katarzyna Cabaj
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
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30
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Spisz P, Kozak W, Chomicz-Mańka L, Makurat S, Falkiewicz K, Sikorski A, Czaja A, Rak J, Zdrowowicz M. 5-( N-Trifluoromethylcarboxy)aminouracil as a Potential DNA Radiosensitizer and Its Radiochemical Conversion into N-Uracil-5-yloxamic Acid. Int J Mol Sci 2020; 21:E6352. [PMID: 32883013 PMCID: PMC7504071 DOI: 10.3390/ijms21176352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/18/2020] [Accepted: 08/28/2020] [Indexed: 01/01/2023] Open
Abstract
Hypoxia-a hallmark of solid tumors-dramatically impairs radiotherapy, one of the most common anticancer modalities. The adverse effect of the low-oxygen state can be eliminated by the concomitant use of a hypoxic cell radiosensitizer. In the present paper, we show that 5-(N-trifluoromethylcarboxy) aminouracil (CF3CONHU) can be considered as an effective radiosensitizer of DNA damage, working under hypoxia. The title compound was synthesized in the reaction of 5-aminouracil and trifluoroacetic anhydride in trifluoroacetic acid. Then, an aqueous and deoxygenated solution of the HPLC purified compound containing tert-butanol as a hydroxyl radical scavenger was irradiated with X-rays. Radiodegradation in a 26.67 ± 0.31% yield resulted in only one major product-N-uracil-5-yloxamic acid. The mechanism that is possibly responsible for the formation of the observed radioproduct has been elucidated with the use of DFT calculations. The cytotoxic test against the PC3 prostate cancer cell line and HDFa human dermal fibroblasts confirmed the low cytotoxicity of CF3CONHU. Finally, a clonogenic assay and flow cytometric analysis of histone H2A.X phosphorylation proved the radiosensitization in vitro.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Magdalena Zdrowowicz
- Department of Physical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (P.S.); (W.K.); (L.C.-M.); (S.M.); (K.F.); (A.S.); (A.C.); (J.R.)
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31
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Rzepiela K, Buczek A, Kupka T, Broda MA. Factors Governing the Chemical Stability and NMR Parameters of Uracil Tautomers and Its 5-Halogen Derivatives. Molecules 2020; 25:E3931. [PMID: 32872098 PMCID: PMC7504704 DOI: 10.3390/molecules25173931] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 01/10/2023] Open
Abstract
We report on the density functional theory (DFT) modelling of structural, energetic and NMR parameters of uracil and its derivatives (5-halogenouracil (5XU), X = F, Cl, Br and I) in vacuum and in water using the polarizable continuum model (PCM) and the solvent model density (SMD) approach. On the basis of the obtained results, we conclude that the intramolecular electrostatic interactions are the main factors governing the stability of the six tautomeric forms of uracil and 5XU. Two indices of aromaticity, the harmonic oscillator model of aromaticity (HOMA), satisfying the geometric criterion, and the nuclear independent chemical shift (NICS), were applied to evaluate the aromaticity of uracil and its derivatives in the gas phase and water. The values of these parameters showed that the most stable tautomer is the least aromatic. A good performance of newly designed xOPBE density functional in combination with both large aug-cc-pVQZ and small STO(1M)-3G basis sets for predicting chemical shifts of uracil and 5-fluorouracil in vacuum and water was observed. As a practical alternative for calculating the chemical shifts of challenging heterocyclic compounds, we also propose B3LYP calculations with small STO(1M)-3G basis set. The indirect spin-spin coupling constants predicted by B3LYP/aug-cc-pVQZ(mixed) method reproduce the experimental data for uracil and 5-fluorouracil well.
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Affiliation(s)
| | | | - Teobald Kupka
- Department of Physical Chemistry and Molecular Modeling, Faculty of Chemistry, University of Opole, 48 Oleska Street, 45−052 Opole, Poland; (K.R.); (A.B.)
| | - Małgorzata A. Broda
- Department of Physical Chemistry and Molecular Modeling, Faculty of Chemistry, University of Opole, 48 Oleska Street, 45−052 Opole, Poland; (K.R.); (A.B.)
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32
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Geant PY, Uttaro JP, Périgaud C, Mathé C. Synthesis and Antiviral Evaluation of 3'-Fluoro-5'-norcarbocyclic Nucleoside Phosphonates Bearing Uracil and Cytosine as Potential Antiviral Agents. Molecules 2020; 25:molecules25163708. [PMID: 32823897 PMCID: PMC7466164 DOI: 10.3390/molecules25163708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/04/2020] [Accepted: 08/12/2020] [Indexed: 12/24/2022] Open
Abstract
Carbocyclic nucleoside analogues are an essential class of antiviral agents and are commonly used in the treatment of viral diseases (hepatitis B, AIDS). Recently, we reported the racemic synthesis and the anti-human immunodeficiency virus activities (HIV) of 3'-fluoro-5'-norcarbocyclic nucleoside phosphonates bearing purines as heterocyclic base. Based on these results, the corresponding racemic norcarbocyclic nucleoside phosphonates bearing pyrimidine bases were synthesized. The prepared compounds were evaluated against HIV, but none of them showed marked antiviral activity compared to their purine counterparts.
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33
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Wieczorkiewicz PA, Szatylowicz H, Krygowski TM. Mutual Relations between Substituent Effect, Hydrogen Bonding, and Aromaticity in Adenine-Uracil and Adenine-Adenine Base Pairs. Molecules 2020; 25:E3688. [PMID: 32823565 PMCID: PMC7464026 DOI: 10.3390/molecules25163688] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 07/30/2020] [Accepted: 08/11/2020] [Indexed: 11/16/2022] Open
Abstract
The electronic structure of substituted molecules is governed, to a significant extent, by the substituent effect (SE). In this paper, SEs in selected nucleic acid base pairs (Watson-Crick, Hoogsteen, adenine-adenine) are analyzed, with special emphasis on their influence on intramolecular interactions, aromaticity, and base pair hydrogen bonding. Quantum chemistry methods-DFT calculations, the natural bond orbital (NBO) approach, the Harmonic Oscillator Model of Aromaticity (HOMA) index, the charge of the substituent active region (cSAR) model, and the quantum theory of atoms in molecules (QTAIM)-are used to compare SEs acting on adenine moiety and H-bonds from various substitution positions. Comparisons of classical SEs in adenine with those observed in para- and meta-substituted benzenes allow for the better interpretation of the obtained results. Hydrogen bond stability and its other characteristics (e.g., covalency) can be significantly changed as a result of the SE, and its consequences are dependent on the substitution position. These changes allow us to investigate specific relations between H-bond parameters, leading to conclusions concerning the nature of hydrogen bonding in adenine dimers-e.g., H-bonds formed by five-membered ring nitrogen acceptor atoms have an inferior, less pronounced covalent nature as compared to those formed by six-membered ring nitrogen. The energies of individual H-bonds (obtained by the NBO method) are analyzed and compared to those predicted by the Espinosa-Molins-Lecomte (EML) model. Moreover, both SE and H-bonds can significantly affect the aromaticity of adenine rings; long-distance SEs on π-electron delocalization are also documented.
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Affiliation(s)
- Paweł A. Wieczorkiewicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
| | - Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
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34
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Ivanov SP, Ostakhov SS, Abdrakhimova GS, Akhiyarov AA, Khursan SL. On the use of the spectral luminescent method for studying acid-base equilibria of uracil derivatives in aqueous solutions. Biophys Chem 2020; 266:106432. [PMID: 32771804 DOI: 10.1016/j.bpc.2020.106432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/07/2020] [Accepted: 07/11/2020] [Indexed: 11/20/2022]
Abstract
The effect of pH on fluorescence parameters (spectral composition, intensity Ifl, and quantum yield φ) of thymine (T), 5-fluorouracil (FU) and 6-aminouracil (AU) have been investigated in aqueous solutions. As found, there is the regularity of the changes in the spectral composition, intensity, and quantum yields of uracil fluorescence depending on pH. The constants of the acid-base equilibria of uracils (pKa) determined by the fluorescence titration method are: 9.9 (T), 8.0 (FU), and 9.1 (AU) at 298 K. These pKa1 values satisfactorily agree with the previous estimates obtained by independent experimental or quantum chemical methods. The possibilities of the spectral fluorescence method for the quantitative description of the acid-base equilibria of uracils depending on the fluorescent features of the pyrimidinedione and its conjugate base are discussed.
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Affiliation(s)
- Sergey P Ivanov
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, 71 Prospekt Oktyabrya, 450054 Ufa, Russian Federation.
| | - Sergei S Ostakhov
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, 71 Prospekt Oktyabrya, 450054 Ufa, Russian Federation
| | - Gulnaz S Abdrakhimova
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, 71 Prospekt Oktyabrya, 450054 Ufa, Russian Federation
| | - Aidar A Akhiyarov
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, 71 Prospekt Oktyabrya, 450054 Ufa, Russian Federation
| | - Sergey L Khursan
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, 71 Prospekt Oktyabrya, 450054 Ufa, Russian Federation
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35
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Abstract
Dynamic and reversible non-covalent interactions endow synthetic systems and materials with smart adaptive functions that allow them to response to diverse stimuli, interact with external agents, or repair structural defects. Inspired by the outstanding performance and selectivity of DNA in living systems, scientists are increasingly employing Watson-Crick nucleobase pairing to control the structure and properties of self-assembled materials. Two sets of complementary purine-pyrimidine pairs (guanine:cytosine and adenine:thymine(uracil)) are available that provide selective and directional H-bonding interactions, present multiple metal-coordination sites, and exhibit rich redox chemistry. In this review, we highlight several recent examples that profit from these features and employ nucleobase interactions in functional systems and materials, covering the fields of energy/electron transfer, charge transport, adaptive nanoparticles, porous materials, macromolecule self-assembly, or polymeric materials with adhesive or self-healing ability.
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Affiliation(s)
- Anselmo del Prado
- Departamento de Química OrgánicaFacultad de CienciasUniversidad Autónoma de Madrid28049MadridSpain
| | - David González‐Rodríguez
- Departamento de Química OrgánicaFacultad de CienciasUniversidad Autónoma de Madrid28049MadridSpain
- Institute for Advanced Research in Chemical Sciences (IAdChem)Universidad Autónoma de Madrid28049MadridSpain
| | - Yi‐Lin Wu
- School of ChemistryCardiff UniversityPark PlaceCardiffCF10 3ATUK
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36
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Corinti D, Crestoni ME, Chiavarino B, Fornarini S, Scuderi D, Salpin JY. Insights into Cisplatin Binding to Uracil and Thiouracils from IRMPD Spectroscopy and Tandem Mass Spectrometry. J Am Soc Mass Spectrom 2020; 31:946-960. [PMID: 32233383 PMCID: PMC7997577 DOI: 10.1021/jasms.0c00006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The monofunctional primary complexes cis-[PtCl(NH3)2(L)]+, formed by the reaction of cisplatin, a major chemotherapeutic agent, with four nucleobases L, i.e., uracil (U), 2-thiouracil (2SU), 4-thiouracil (4SU), and 2,4-dithiouracil (24dSU), have been studied by a combination of infrared multiple photon dissociation (IRMPD) action spectroscopy in both the fingerprint (900-1900 cm-1) and the N-H/O-H stretching (3000-3800 cm-1) ranges, energy-resolved collision-induced dissociation (CID) mass spectrometry, and density functional calculations at the B3LYP/LACVP/6-311G** level. On the basis of the comparison across the experimental features and the linear IR spectra of conceivable structures, the cisplatin residue is found to promote a monodentate interaction preferentially with the O4(S4) atoms of the canonical forms of U, 4SU, and 24dSU and to the S2 atom of 2SU, yielding the most stable structures. Additional absorptions reveal the presence of minor, alternative tautomers in the sampled ion populations of 2SU and 24dSU, underlying the ability of cisplatin to increase the prospect of (therapeutically beneficial) nucleic acid strand disorder. Implication of these evidence may provide insights into drug mechanism and design.
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Affiliation(s)
- Davide Corinti
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, P. le A. Moro 5, Roma 00185, Italy
| | - Maria Elisa Crestoni
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, P. le A. Moro 5, Roma 00185, Italy
| | - Barbara Chiavarino
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, P. le A. Moro 5, Roma 00185, Italy
| | - Simonetta Fornarini
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, P. le A. Moro 5, Roma 00185, Italy
| | - Debora Scuderi
- Universite′
Paris-Saclay, CNRS, Institut de Chimie Physique
UMR8000, Orsay 91405, France
| | - Jean-Yves Salpin
- Université
Paris-Saclay, CNRS, Univ Evry,
LAMBE, Evry-Courcouronnes 91025, France
- CY
Cergy Paris Université, LAMBE, Evry-Courcouronnes 91025, France
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37
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Fu S, Zhang Y, Yang C, Meng Q. Preparation of Uracil by bacteria isolated from Morchella. Pak J Pharm Sci 2020; 33:621-625. [PMID: 32276907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Morchella is one of the most famous rare edible and medicinal fungi over the world. Highly nutritious and immature cultivation techniques led to the high price and the markets have remained tight. The pathogenic bacteria were serious in artificial cultivation of Morchella that affected the growth and yield of Morchella. Isolation of pathogenic bacteria and metabolites were investigated in order to improve the artificial cultivation technology. The isolated strain (YDJZ-01-01C) was identified by Gram staining and sequence of 16S rDNA. Structures of metabolites were confirmed based on NMR spectra and literatures. However, the main products were uracil and thymine that considered as important intermediate of anti-tumor 5-fluorouracil. Interestingly, a new synthetic pathway for preparation of uracil by microorganism was found except for chemical synthesis. The new preparation pathway provided mild, green, sustainable and environment friendly method to produce uracil that meets the needs of modern chemistry.
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Affiliation(s)
- Shaobin Fu
- Department of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Ye Zhang
- Department of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Cailing Yang
- Department of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Qingfeng Meng
- Department of Public Health, Zunyi Medical University, Zunyi, China
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38
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Elshakre ME, Noamaan MA, Moustafa H, Butt H. Density Functional Theory, Chemical Reactivity, Pharmacological Potential and Molecular Docking of Dihydrothiouracil-Indenopyridopyrimidines with Human-DNA Topoisomerase II. Int J Mol Sci 2020; 21:E1253. [PMID: 32070048 PMCID: PMC7072893 DOI: 10.3390/ijms21041253] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/25/2020] [Accepted: 01/27/2020] [Indexed: 01/31/2023] Open
Abstract
In this work, three computational methods (Hatree-Fock (HF), Møller-Plesset 2 (MP2), and Density Functional Theory (DFT)) using a variety of basis sets are used to determine the atomic and molecular properties of dihydrothiouracil-based indenopyridopyrimidine (TUDHIPP) derivatives. Reactivity descriptors of this system, including chemical potential (µ), chemical hardness (η), electrophilicity (ω), condensed Fukui function and dual descriptors are calculated at B3LYP/6-311++ G (d,p) to identify reactivity changes of these molecules in both gas and aqueous phases. We determined the molecular electrostatic surface potential (MESP) to determine the most active site in these molecules. Molecular docking study of TUDHIPP with topoisomerase II α and β is performed, predicting binding sites and binding energies with amino acids of both proteins. Docking studies of TUDHIPP versus etoposide suggest their potential as antitumor candidates. We have applied Lipinski, Veber's rules and analysis of the Golden triangle and structure activity/property relationship for a series of TUDHIPP derivatives indicate that the proposed compounds exhibit good oral bioavailability. The comparison of the drug likeness descriptors of TUDHIPP with those of etoposide, which is known to be an antitumor drug, indicates that TUDHIPP can be considered as an antitumor drug. The overall study indicates that TUDHIPP has comparable and even better descriptors than etoposide proposing that it can be as effective antitumor drug, especially 2H, 6H and 7H compounds.
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Affiliation(s)
- Mohamed E. Elshakre
- Chemistry Department, College of Science, Cairo University, Cairo 12613, Egypt;
| | - Mahmoud A. Noamaan
- Chemistry Department, College of Science, Cairo University, Cairo 12613, Egypt;
| | - Hussein Moustafa
- Chemistry Department, College of Science, Cairo University, Cairo 12613, Egypt;
| | - Haider Butt
- Department of Mechanical Engineering, Khalifa University, Abu Dhabi 127788, UAE;
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39
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Jeong H, Oh K. Uracil-doped DNA thin solid films: a new way to control optical dispersion of DNA film using a RNA constituent. Opt Express 2019; 27:36075-36087. [PMID: 31873394 DOI: 10.1364/oe.27.036075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023]
Abstract
Among five nucleobases, adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U), uracil is a key distinctive constituent existing only in ribonucleic acid (RNA). RNA shares the common A, G, and C with deoxyribonucleic acid (DNA) made of A-T, G-C hydrogen bonding. We explored a new attempt to combine uracil (U) with DNA, successfully realizing U-doped DNA thin solid films for the first time. Impacts of uracil on optical properties of the films were thoroughly investigated. The method was based on optimal spin-coating of an aqueous solution of DNA and uracil over silicon or silica substrates. Optical absorption of both aqueous solution and U-doped DNA thin solid films was characterized in a wide spectral range covering UV-visible-IR. Immobilization of uracil within DNA thin solid films was experimentally confirmed by FTIR spectroscopy studies. By using an ellipsometer, we measured the refractive indices of the films and discovered that U-doping was a very effective means to control optical dispersion DNA thin solid film. We further investigated thermo-optic behavior to find impacts of U-doping in DNA films. Detailed thin film processes and optical characterizations are discussed.
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40
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Hölz K, Pavlic A, Lietard J, Somoza MM. Specificity and Efficiency of the Uracil DNA Glycosylase-Mediated Strand Cleavage Surveyed on Large Sequence Libraries. Sci Rep 2019; 9:17822. [PMID: 31780717 PMCID: PMC6883067 DOI: 10.1038/s41598-019-54044-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/07/2019] [Indexed: 02/07/2023] Open
Abstract
Uracil-DNA glycosylase (UDG) is a critical DNA repair enzyme that is well conserved and ubiquitous in nearly all life forms. UDG protects genomic information integrity by catalyzing the excision from DNA of uracil nucleobases resulting from misincorporation or spontaneous cytosine deamination. UDG-mediated strand cleavage is also an important tool in molecular biotechnology, allowing for controlled and location-specific cleavage of single- and double DNA chemically or enzymatically synthesized with single or multiple incorporations of deoxyuridine. Although the cleavage mechanism is well-understood, detailed knowledge of efficiency and sequence specificity, in both single and double-stranded DNA contexts, has so far remained incomplete. Here we use an experimental approach based on the large-scale photolithographic synthesis of uracil-containing DNA oligonucleotides to comprehensively probe the context-dependent uracil excision efficiency of UDG.
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Affiliation(s)
- Kathrin Hölz
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Angelina Pavlic
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Jory Lietard
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
| | - Mark M Somoza
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
- Chair of Food Chemistry and Molecular and Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, D-85354, Freising, Germany.
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41
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Semenov VE, Zueva IV, Lushchekina SV, Lenina OA, Gubaidullina LM, Saifina LF, Shulaeva MM, Kayumova RM, Saifina AF, Gubaidullin AT, Kondrashova SA, Latypov SK, Masson P, Petrov KA. 6-Methyluracil derivatives as peripheral site ligand-hydroxamic acid conjugates: Reactivation for paraoxon-inhibited acetylcholinesterase. Eur J Med Chem 2019; 185:111787. [PMID: 31675511 DOI: 10.1016/j.ejmech.2019.111787] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/07/2019] [Accepted: 10/11/2019] [Indexed: 12/19/2022]
Abstract
New uncharged conjugates of 6-methyluracil derivatives with imidazole-2-aldoxime and 1,2,4-triazole-3-hydroxamic acid units were synthesized and studied as reactivators of organophosphate-inhibited cholinesterase. Using paraoxon (POX) as a model organophosphate, it was shown that 6-methyluracil derivatives linked with hydroxamic acid are able to reactivate POX-inhibited human acetylcholinesterase (AChE) in vitro. The reactivating efficacy of one compound (5b) is lower than that of pyridinium-2-aldoxime (2-PAM). Meanwhile, unlike 2-PAM, in vivo study showed that the lead compound 5b is able: (1) to reactivate POX-inhibited AChE in the brain; (2) to decrease death of neurons and, (3) to prevent memory impairment in rat model of POX-induced neurodegeneration.
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Affiliation(s)
- Vyacheslav E Semenov
- Arbuzov Institute of Organic and Physical Chemistry, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Arbuzov str., 8, Kazan, 420088, Russian Federation.
| | - Irina V Zueva
- Arbuzov Institute of Organic and Physical Chemistry, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Arbuzov str., 8, Kazan, 420088, Russian Federation
| | - Sofya V Lushchekina
- N.M. Emanuel Institute of Biochemical Physics of Russian Academy of Sciences, Kosygina str., 4, Moscow, 119334, Russian Federation
| | - Oksana A Lenina
- Arbuzov Institute of Organic and Physical Chemistry, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Arbuzov str., 8, Kazan, 420088, Russian Federation
| | - Lilya M Gubaidullina
- Arbuzov Institute of Organic and Physical Chemistry, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Arbuzov str., 8, Kazan, 420088, Russian Federation
| | - Lilya F Saifina
- Arbuzov Institute of Organic and Physical Chemistry, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Arbuzov str., 8, Kazan, 420088, Russian Federation
| | - Marina M Shulaeva
- Arbuzov Institute of Organic and Physical Chemistry, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Arbuzov str., 8, Kazan, 420088, Russian Federation
| | - Ramilya M Kayumova
- Arbuzov Institute of Organic and Physical Chemistry, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Arbuzov str., 8, Kazan, 420088, Russian Federation
| | - Alina F Saifina
- Arbuzov Institute of Organic and Physical Chemistry, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Arbuzov str., 8, Kazan, 420088, Russian Federation
| | - Aidar T Gubaidullin
- Arbuzov Institute of Organic and Physical Chemistry, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Arbuzov str., 8, Kazan, 420088, Russian Federation
| | - Svetlana A Kondrashova
- Arbuzov Institute of Organic and Physical Chemistry, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Arbuzov str., 8, Kazan, 420088, Russian Federation
| | - Shamil K Latypov
- Arbuzov Institute of Organic and Physical Chemistry, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Arbuzov str., 8, Kazan, 420088, Russian Federation
| | - Patrick Masson
- Kazan Federal University, Kremlyovskaya str., 18, Kazan, 420008, Russian Federation
| | - Konstantin A Petrov
- Arbuzov Institute of Organic and Physical Chemistry, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Arbuzov str., 8, Kazan, 420088, Russian Federation
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42
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Cheng CC, Gebeyehu BT, Huang SY, Abebe Alemayehu Y, Sun YT, Lai YC, Chang YH, Lai JY, Lee DJ. Entrapment of an adenine derivative by a photo-irradiated uracil-functionalized micelle confers controlled self-assembly behavior. J Colloid Interface Sci 2019; 552:166-178. [PMID: 31125827 DOI: 10.1016/j.jcis.2019.05.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/17/2019] [Accepted: 05/18/2019] [Indexed: 11/15/2022]
Abstract
HYPOTHESIS Invoking cooperative assembly of the uracil-functionalized supramolecular polymer BU-PPG [uracil end-capped poly(propylene glycol)] upon association with the nucleobase adenine derivative A-MA [methyl 3-(6-amino-9H-purin-9-yl)propanoate] as a model drug provides a new concept to control and tune the properties of supramolecular complexes and holds significant potential for the development of safer, more effective drug delivery systems. EXPERIMENTS BU-PPG and A-MA were successfully developed and exhibited specific recognition and high affinity, which enabled reversible complementary adenine-uracil (A-U) hydrogen bonding-induced formation of spherical micelles in aqueous solution. The self-assembly and controllable A-MA release behavior of BU-PPG/A-MA micelles were studied using morphological analysis and optical and light scattering techniques to investigate the effect of photoirradiation and temperature on the complementary hydrogen bond interactions between BU-PPG and A-MA. FINDINGS The resulting micelles possess unusual physical properties, including controlled photoreactivity kinetics, controllable self-assembled morphology and low cytotoxicity in vitro, as well as reversible temperature-responsive behavior. Importantly, irradiated micelles exhibited excellent long-term structural stability under normal physiological conditions and serum disturbance. Increasing the temperature triggered rapid release of A-MA by disrupting A-U complexes. These findings represent an entirely new, promising strategy for the development of multi-controlled release drug delivery nanocarriers based on complementary hydrogen bonding interactions.
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Affiliation(s)
- Chih-Chia Cheng
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan; Advanced Membrane Materials Research Center, National Taiwan University of Science and Technology, Taipei 10607, Taiwan.
| | - Belete Tewabe Gebeyehu
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Shan-You Huang
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Yihalem Abebe Alemayehu
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Ya-Ting Sun
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - You-Cheng Lai
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Yi-Hsuan Chang
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Juin-Yih Lai
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan; Advanced Membrane Materials Research Center, National Taiwan University of Science and Technology, Taipei 10607, Taiwan; Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan; R&D Center for Membrane Technology, Chung Yuan Christian University, Chungli, Taoyuan 32043, Taiwan
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan; Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
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Takenaga N, Hayashi T, Ueda S, Satake H, Yamada Y, Kodama T, Dohi AT. Synthesis of Uracil-Iodonium(III) Salts for Practical Utilization as Nucleobase Synthetic Modules. Molecules 2019; 24:molecules24173034. [PMID: 31438596 PMCID: PMC6749211 DOI: 10.3390/molecules24173034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/16/2019] [Accepted: 08/19/2019] [Indexed: 01/08/2023] Open
Abstract
Iodonium(III) salts bearing uracil moieties have recently appeared in the literature, but their structural scope and utilization are limited because of their hygroscopic characteristics. In this study, we describe our detailed investigations for synthesizing a series of uracil iodonium(III) salts derived with various structural motifs and counterions. These new compounds have been utilized as attractive synthetic modules in constructing functionalized nucleobase and nucleosides.
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Affiliation(s)
- Naoko Takenaga
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya 468-8503, Japan.
| | - Takumi Hayashi
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Shohei Ueda
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Hiroyuki Satake
- Department of Liberal Arts and Sciences, Kanagawa University of Human Services, 1-10-1 Heisei-cho, Yokosuka, Kanagawa 238-8522, Japan
| | - Yoichi Yamada
- School of Pharmacy, Shujitsu University, 1-6-1 Nishigawara, Naka-ku, Okayama 703-8516, Japan
| | - Tetsuya Kodama
- Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - And Toshifumi Dohi
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan.
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44
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León C, Boix C, Beltrán E, Peñuela G, López F, Sancho JV, Hernández F. Study of cyanotoxin degradation and evaluation of their transformation products in surface waters by LC-QTOF MS. Chemosphere 2019; 229:538-548. [PMID: 31100625 DOI: 10.1016/j.chemosphere.2019.04.219] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
In the present work, the degradation of three cyanotoxins from the hepatotoxins group was investigated under laboratory-controlled experiments in water samples. Surface waters spiked with microcystin-LR (MC-LR), nodularin (NOD) and cylindrospermopsin (CYN) were subjected to hydrolysis, chlorination and photo-degradation, under both sunlight (SL) and ultraviolet (UV) radiation. A total of 12 transformation products (TPs) were detected and tentatively identified by liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC-QTOF MS). These comprised: 6 chlorination TPs (3 from CYN and 3 from MC-LR, 2 isomers); 4 UV TPs (all from CYN); and 2 sunlight TPs (one isomer from MC-LR and another from NOD). No TPs were observed under hydrolysis conditions. The chemical structures for all TPs were tentatively proposed based on the accurate-mass QTOF MS full-spectra. Analysis of real-world samples collected from the Peñol reservoir (Antioquia, Colombia) revealed the presence of MC-LR and CYN as well as a sunlight TP identified in the laboratory experiments. Data presented in this article will assist further research on TPs potentially formed in future tertiary degradation processes applied for the removal of organic micro-pollutants in water; as well as improving available knowledge on the toxic implications of cyanobacterial toxins TPs in surface waters.
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Affiliation(s)
- Cristina León
- Grupo Diagnóstico y Control de La Contaminación (GDCON), Facultad de Ingeniería Universidad de Antioquia, Medellín, Colombia.
| | - Clara Boix
- Research Institute for Pesticides and Water (IUPA), University Jaume I. Avda, Sos Baynat, E-12071 Castellon, Spain
| | - Eduardo Beltrán
- Research Institute for Pesticides and Water (IUPA), University Jaume I. Avda, Sos Baynat, E-12071 Castellon, Spain
| | - Gustavo Peñuela
- Grupo Diagnóstico y Control de La Contaminación (GDCON), Facultad de Ingeniería Universidad de Antioquia, Medellín, Colombia
| | - Francisco López
- Research Institute for Pesticides and Water (IUPA), University Jaume I. Avda, Sos Baynat, E-12071 Castellon, Spain
| | - Juan V Sancho
- Research Institute for Pesticides and Water (IUPA), University Jaume I. Avda, Sos Baynat, E-12071 Castellon, Spain
| | - Félix Hernández
- Research Institute for Pesticides and Water (IUPA), University Jaume I. Avda, Sos Baynat, E-12071 Castellon, Spain.
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45
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Stathi A, Mamais M, Chrysina ED, Gimisis T. Anomeric Spironucleosides of β-d-Glucopyranosyl Uracil as Potential Inhibitors of Glycogen Phosphorylase. Molecules 2019; 24:E2327. [PMID: 31242546 PMCID: PMC6630470 DOI: 10.3390/molecules24122327] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 11/16/2022] Open
Abstract
In the case of type 2 diabetes, inhibitors of glycogen phosphorylase (GP) may prevent unwanted glycogenolysis under high glucose conditions and thus aim at the reduction of excessive glucose production by the liver. Anomeric spironucleosides, such as hydantocidin, present a rich synthetic chemistry and important biological function (e.g., inhibition of GP). For this study, the Suárez radical methodology was successfully applied to synthesize the first example of a 1,6-dioxa-4-azaspiro[4.5]decane system, not previously constructed via a radical pathway, starting from 6-hydroxymethyl-β-d-glucopyranosyluracil. It was shown that, in the rigid pyranosyl conformation, the required [1,5]-radical translocation was a minor process. The stereochemistry of the spirocycles obtained was unequivocally determined based on the chemical shifts of key sugar protons in the 1H-NMR spectra. The two spirocycles were found to be modest inhibitors of RMGPb.
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Affiliation(s)
- Aggeliki Stathi
- Organic Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, 10571 Athens, Greece.
| | - Michael Mamais
- Organic Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, 10571 Athens, Greece.
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece.
| | - Evangelia D Chrysina
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece.
| | - Thanasis Gimisis
- Organic Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, 10571 Athens, Greece.
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46
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Marx D, Schnakenburg G, Grimme S, Müller CE. Structural and Conformational Studies on Carboxamides of 5,6-Diaminouracils-Precursors of Biologically Active Xanthine Derivatives. Molecules 2019; 24:molecules24112168. [PMID: 31181839 PMCID: PMC6600361 DOI: 10.3390/molecules24112168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/02/2019] [Accepted: 06/04/2019] [Indexed: 11/16/2022] Open
Abstract
8-Arylethynylxanthine derivatives are potent, selective adenosine A2A receptor antagonists, which represent (potential) therapeutics for Parkinson's disease, Alzheimer's dementia, and the immunotherapy of cancer. 6-Amino-5-amidouracil derivatives are important precursors for the synthesis of such xanthines. We noticed an unexpected duplication of NMR signals in many of these uracil derivatives. Here, we present a detailed analytical study of structurally diverse 6-amino-5-carboxamidouracils employing dynamic and two-dimensional NMR spectroscopy, density functional theory calculations, and X-ray analysis to explain the unexpected properties of these valuable drug intermediates.
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Affiliation(s)
- Daniel Marx
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, D-53121 Bonn, Germany.
- Pharma Center Bonn, University of Bonn, D-53121 Bonn, Germany.
| | - Gregor Schnakenburg
- Department of Chemistry, Institute of Inorganic Chemistry, University of Bonn, D-53121 Bonn, Germany.
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, D-53115 Bonn, Germany.
| | - Christa E Müller
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, D-53121 Bonn, Germany.
- Pharma Center Bonn, University of Bonn, D-53121 Bonn, Germany.
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47
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Brister MM, Crespo-Hernández CE. Excited-State Dynamics in the RNA Nucleotide Uridine 5'-Monophosphate Investigated Using Femtosecond Broadband Transient Absorption Spectroscopy. J Phys Chem Lett 2019; 10:2156-2161. [PMID: 30995048 DOI: 10.1021/acs.jpclett.9b00492] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Damage to RNA from ultraviolet radiation induces chemical modifications to the nucleobases. Unraveling the excited states involved in these reactions is essential; however, investigations aimed at understanding the electronic-energy relaxation pathways of the RNA nucleotide uridine 5'-monophosphate (UMP) have not received enough attention. In this Letter, the excited-state dynamics of UMP is investigated in aqueous solution. Excitation at 267 nm results in a trifurcation event that leads to the simultaneous population of the vibrationally excited ground state, a long-lived 1nπ* state, and a receiver triplet state within 200 fs. The receiver state internally converts to the long-lived 3ππ* state in an ultrafast time scale. The results elucidate the electronic relaxation pathways and clarify earlier transient absorption experiments performed for uracil derivatives in solution. This mechanistic information is important because long-lived nπ* and ππ* excited states of both singlet and triplet multiplicities are thought to lead to the formation of harmful photoproducts.
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Affiliation(s)
- Matthew M Brister
- Department of Chemistry , Case Western Reserve University , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States
| | - Carlos E Crespo-Hernández
- Department of Chemistry , Case Western Reserve University , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States
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48
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Chistov AA, Orlov AA, Streshnev PP, Slesarchuk NA, Aparin IO, Rathi B, Brylev VA, Kutyakov SV, Mikhura IV, Ustinov AV, Westman G, Palyulin VA, Jain N, Osolodkin DI, Kozlovskaya LI, Korshun VA. Compounds based on 5-(perylen-3-ylethynyl)uracil scaffold: High activity against tick-borne encephalitis virus and non-specific activity against enterovirus A. Eur J Med Chem 2019; 171:93-103. [PMID: 30909022 DOI: 10.1016/j.ejmech.2019.03.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 02/17/2019] [Accepted: 03/12/2019] [Indexed: 12/26/2022]
Abstract
Rigid amphipathic fusion inhibitors (RAFIs) are potent antivirals based on a perylene core linked with a nucleoside moiety. Sugar-free analogues of RAFIs, 5-(perylen-3-ylethynyl)uracil-1-acetic acid 1 and its amides 2, were synthesized using combined protection group strategy. Compounds 1 and 2 appeared to have low toxicity on porcine embryo kidney (PEK) or rhabdomiosarcoma (RD) cells together with remarkable activity against enveloped tick-borne encephalitis virus (TBEV): EC50 values vary from 0.077 μM to subnanomolar range. Surprisingly, 3-pivaloyloxymethyl (Pom) protected precursors 7 and 8 showed even more pronounced activity. All the compounds showed no activity against several non-enveloped enteroviruses, except 4-hydroxybutylamides 2d,g, which inhibited the reproduction of enterovirus A71 with EC50 50-100 μM, with a non-specific mode of action. The results suggest that the carbohydrate moiety of RAFI nucleosides does not play a crucial role in their antiviral action, and biological activity of the 5-(perylen-3-ylethynyl)uracil scaffold can be effectively modulated by substituents in positions 1 and 3. The high antiviral activity of these new compounds, coupled with low toxicity advocate their potential role in antiviral therapy.
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Affiliation(s)
- Alexey A Chistov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Alexey A Orlov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia; FSBSI "Chumakov FSC R&D IBP RAS", 8 bd 1 Poselok Instituta Poliomielita, Poselenie Moskovsky, Moscow 108819, Russia; Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bd 3, Moscow 119992, Russia
| | - Philipp P Streshnev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Nikita A Slesarchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Ilya O Aparin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia; Skolkovo Institute of Science and Technology, Skolkovo, Moscow 143026, Russia
| | - Brijesh Rathi
- Department of Chemistry, Laboratory for Translational Chemistry and Drug Discovery, Hansraj College University Enclave, University of Delhi, Delhi 110007, India
| | - Vladimir A Brylev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia; Biotech Innovations Ltd, Leninskie gory 1 bd 75, Moscow 119992, Russia
| | - Sergey V Kutyakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Irina V Mikhura
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Alexey V Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Gunnar Westman
- Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Vladimir A Palyulin
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bd 3, Moscow 119992, Russia
| | - Nidhi Jain
- Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - Dmitry I Osolodkin
- FSBSI "Chumakov FSC R&D IBP RAS", 8 bd 1 Poselok Instituta Poliomielita, Poselenie Moskovsky, Moscow 108819, Russia; Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bd 3, Moscow 119992, Russia; Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Liubov I Kozlovskaya
- FSBSI "Chumakov FSC R&D IBP RAS", 8 bd 1 Poselok Instituta Poliomielita, Poselenie Moskovsky, Moscow 108819, Russia; Sechenov First Moscow State Medical University, Moscow 119991, Russia.
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia.
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Abstract
Induced pluripotent stem cells (iPSCs) have demonstrated tremendous potential in numerous disease modeling and regenerative medicine-based therapies. The development of innovative gene transduction and editing technologies has further augmented the potential of iPSCs. Cas9-cytidine deaminases, for example, have developed as an alternative strategy to integrate single-base mutations (C → T or G → A transitions) at specific genomic loci. In this chapter, we specifically describe CRISPR (clustered regularly interspaced short palindromic repeats) base editing in iPSCs for editing precise locations in the genome. This state-of-the-art approach enables highly efficient and accurate modifications in genes. Thus, this technique not only has the potential to have biotechnology and therapeutic applications but also the ability to reveal underlying mechanisms regarding pathologies caused by specific mutations.
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Affiliation(s)
- Ya-Ju Chang
- Department of Ophthalmology, Columbia University, New York, NY, USA
- Jonas Children's Vision Care, Bernard and Shirlee Brown Glaucoma Laboratory, Columbia University, New York, NY, USA
| | - Christine L Xu
- Department of Ophthalmology, Columbia University, New York, NY, USA
- Jonas Children's Vision Care, Bernard and Shirlee Brown Glaucoma Laboratory, Columbia University, New York, NY, USA
| | - Xuan Cui
- Department of Ophthalmology, Columbia University, New York, NY, USA
- Jonas Children's Vision Care, Bernard and Shirlee Brown Glaucoma Laboratory, Columbia University, New York, NY, USA
| | - Alexander G Bassuk
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
- Department of Neurology, University of Iowa, Iowa City, IA, USA
| | - Vinit B Mahajan
- Palo Alto Veterans Administration, Palo Alto, CA, USA
- Omics Lab, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA
| | - Yi-Ting Tsai
- Department of Ophthalmology, Columbia University, New York, NY, USA
- Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University, New York, NY, USA.
- Jonas Children's Vision Care, Bernard and Shirlee Brown Glaucoma Laboratory, Columbia University, New York, NY, USA.
- Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
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50
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Mitchell D, Renda AJ, Douds CA, Babitzke P, Assmann SM, Bevilacqua PC. In vivo RNA structural probing of uracil and guanine base-pairing by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). RNA 2019; 25:147-157. [PMID: 30341176 PMCID: PMC6298566 DOI: 10.1261/rna.067868.118] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/18/2018] [Indexed: 05/09/2023]
Abstract
Many biological functions performed by RNAs arise from their in vivo structures. The structure of the same RNA can differ in vitro and in vivo owing in part to the influence of molecules ranging from protons to secondary metabolites to proteins. Chemical reagents that modify the Watson-Crick (WC) face of unprotected RNA bases report on the absence of base-pairing and so are of value to determining structures adopted by RNAs. Reagents have thus been sought that can report on the native RNA structures that prevail in living cells. Dimethyl sulfate (DMS) and glyoxal penetrate cell membranes and inform on RNA secondary structure in vivo through modification of adenine (A), cytosine (C), and guanine (G) bases. Uracil (U) bases, however, have thus far eluded characterization in vivo. Herein, we show that the water-soluble carbodiimide 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) is capable of modifying the WC face of U and G in vivo, favoring the former nucleobase by a factor of ∼1.5, and doing so in the eukaryote rice, as well as in the Gram-negative bacterium Escherichia coli While both EDC and glyoxal target Gs, EDC reacts with Gs in their typical neutral state, while glyoxal requires Gs to populate the rare anionic state. EDC may thus be more generally useful; however, comparison of the reactivity of EDC and glyoxal may allow the identification of Gs with perturbed pKas in vivo and genome-wide. Overall, use of EDC with DMS allows in vivo probing of the base-pairing status of all four RNA bases.
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MESH Headings
- Base Pairing
- Base Sequence
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Ethyldimethylaminopropyl Carbodiimide
- Glyoxal
- Guanine/chemistry
- Indicators and Reagents
- Molecular Probe Techniques
- Molecular Probes
- Molecular Structure
- Nucleic Acid Conformation
- Oryza/chemistry
- Oryza/genetics
- RNA/chemistry
- RNA/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- Uracil/chemistry
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Affiliation(s)
- David Mitchell
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Andrew J Renda
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Catherine A Douds
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Paul Babitzke
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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