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Jezuita A, Wieczorkiewicz PA, Krygowski TM, Szatylowicz H. Influence of the Solvent on the Stability of Aminopurine Tautomers and Properties of the Amino Group. Molecules 2023; 28:molecules28072993. [PMID: 37049758 PMCID: PMC10095612 DOI: 10.3390/molecules28072993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Amino derivatives of purine (2-, 6-, 8-, and N-NH2) have found many applications in biochemistry. This paper presents the results of a systematic computational study of the substituent and solvent effects in these systems. The issues considered are the electron-donating properties of NH2, its geometry, π-electron delocalization in purine rings and tautomeric stability. Calculations were performed in ten environments, with 1 < ε < 109, using the polarizable continuum model of solvation. Electron-donating properties were quantitatively described by cSAR (charge of the substituent active region) parameter and π-electron delocalization by using the HOMA (harmonic oscillator model of aromaticity) index. In aminopurines, NH2 proximity interactions depend on its position and the tautomer. The results show that they are the main factor determining how solvation affects the electron-donating strength and geometry of NH2. Proximity with the NH∙∙∙HN repulsive interaction between the NH2 and endocyclic NH group results in stronger solvent effects than the proximity with two attractive NH∙∙∙N interactions. The effect of amino and nitro (previously studied) substitution on aromaticity was compared; these two groups have, in most cases, the opposite effect, with the largest being in N1H and N3H purine tautomers. The amino group has a smaller effect on the tautomeric preferences of purine than the nitro group. Only in 8-aminopurine do tautomeric preferences change: N7H is more stable than N9H in H2O.
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Affiliation(s)
- Anna Jezuita
- Faculty of Science and Technology, Jan Dlugosz University in Czestochowa, Al. Armii Krajowej 13/15, 42-200 Czestochowa, Poland
| | - Paweł A. Wieczorkiewicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
- Correspondence: (P.A.W.); (H.S.)
| | | | - Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
- Correspondence: (P.A.W.); (H.S.)
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Gorb L, Shishkin OV, Zubatiuk T. The Structure of DNA Fragments: Quantum-Chemical Modelling. BBA ADVANCES 2023; 3:100082. [PMID: 37082263 PMCID: PMC10074966 DOI: 10.1016/j.bbadva.2023.100082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023] Open
Abstract
In this review, we analyze and systematize our computational studies of the nucleic acid duplex formations and thermodynamic stability under the different factors of investigation. The proposed structural models of mini-helix contains N nucleobase pairs (N = 3-5); QM structural data suggest that the helical conformations of mini-helix adopt geometrical parameters comparable to those of natural A- and B-DNA forms under specific conditions as micro hydration and charge compensation. The gas-phase models adopt non regular conformations between the helical form and a ladder form.. The natural helical shape of DNA mini-helix is stabilized by the presence of counterions or by explicit micro-hydration of the major and minor groves. The presence of aqueous solution is shown as a minor factor for the helical shape formation. The studies are performed at the level of density functional theory.
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Affiliation(s)
- Leonid Gorb
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnogo str., 03680 Kyiv, Ukraine
- QSAR Lab Ltd., Trzy Lipy 3, B, 80-172 Gdańsk, Poland
- Corresponding author
| | - Oleg V. Shishkin
- State Scientific Institution “Institute for Single Crystals” of National Academy of Sciences of Ukraine, Nauky Av. 60, 61072 Kharkiv, Ukraine
| | - Tetiana Zubatiuk
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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Pedraza-González L, Charry J, Quintero W, Alí-Torres J, Reyes A. Fast and accurate prediction of proton affinities: revisiting the extended Koopmans' theorem for protons. Phys Chem Chem Phys 2017; 19:25324-25333. [PMID: 28890980 DOI: 10.1039/c7cp04936f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work we propose schemes based on the extended Koopmans' theorem for quantum nuclei (eKT), in the framework of the any particle molecular orbital approach (APMO/KT), for the quantitative prediction of gas phase proton affinities (PAs). The performance of these schemes has been tested on a set of 300 organic molecules containing diverse functional groups. The APMO/KT scheme scaled by functional group (APMO/KT-SC-FG) displays an overall mean absolute error of 1.1 kcal mol-1 with respect to experimental data. Its performance in PA calculations is similar to that of post-Hartree-Fock composite methods or that of the APMO second order proton propagator (APMO/PP2) approach. The APMO/KT-SC-FG scheme is also employed to predict PAs of polyfunctional molecules such as the Nerve Agent VX and the 20 common α-amino acids, finding excellent agreement with available theoretical and/or experimental data. The accuracy of the predictions demonstrates that the APMO/KT-SC-FG scheme is a low-cost alternative to adiabatic methods for the calculation of accurate PAs. One of the most appealing features of the APMO/KT-SC-FG scheme, is that PAs can be derived from one single-point APMO Hartree-Fock calculation.
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Affiliation(s)
- Laura Pedraza-González
- Department of Chemistry, Universidad Nacional de Colombia, Av. Cra 30 # 45-03, Bogotá, Colombia.
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Yurenko YP, Novotný J, Sklenář V, Marek R. Substituting CF2 for O4' in Components of Nucleic Acids: Towards Systems with Reduced Propensity to Form Abasic Lesions. Chemistry 2015; 21:17933-43. [PMID: 26493955 DOI: 10.1002/chem.201502977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Indexed: 01/22/2023]
Abstract
Intrinsic structural features and energetics of nucleotides containing variously fluorinated sugars as potential building blocks of DNA duplexes and quadruplexes are explored systematically using the modern methods of density functional theory (DFT) and quantum chemical topology (QCT). Our results suggest that fluorination at the 2'-β or 2'-α,β positions somewhat stabilizes in vacuo the AI relative to the BI conformations. In contrast, substitution of the CF2 group for the O4' atom (O4'-CF2 modification) leads to a preference of the BI relative to AI DNA-like conformers. All the studied modifications result in a noticeable increase in the stability of the glycosidic bond [estimated by the relaxed force constants (RFC) approach], with particularly encouraging results for the O4'-CF2 derivative. Consequently, the O4'-CF2 modified systems are suggested and explored as promising scaffolds for the development of duplex and quadruplex structures with reduced propensity to form abasic lesions and to undergo DNA damage.
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Affiliation(s)
- Yevgen P Yurenko
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic).
| | - Jan Novotný
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic)
| | - Vladimir Sklenář
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic).,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic).,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic)
| | - Radek Marek
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic). .,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic). .,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno (Czech Republic).
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Synthesis, G-quadruplexes DNA binding, and photocytotoxicity of novel cationic expanded porphyrins. Bioorg Chem 2015; 60:110-7. [DOI: 10.1016/j.bioorg.2015.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/29/2015] [Accepted: 05/01/2015] [Indexed: 11/23/2022]
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Mechanisms for the synthesis of conjugated enynes from diphenylacetylene and trimethylsilylacetylene catalyzed by a nickel(0) complex: DFT study of ligand-controlled selectivity. J Mol Model 2015; 21:135. [DOI: 10.1007/s00894-015-2672-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 03/31/2015] [Indexed: 10/23/2022]
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The effect of intramolecular hydrogen bond on the N-glycosidic bond strength in 3-methyl-2′-deoxyadenosine: a quantum chemical study. Struct Chem 2014. [DOI: 10.1007/s11224-014-0493-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Fujiwara SI, Sawada K, Amisaki T. Molecular dynamics study on conformational differences between dGMP and 8-oxo-dGMP: Effects of metal ions. J Mol Graph Model 2014; 51:158-67. [PMID: 24929814 DOI: 10.1016/j.jmgm.2014.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 05/09/2014] [Accepted: 05/22/2014] [Indexed: 01/05/2023]
Abstract
The modified nucleotide base 7,8-dihydro-8-oxo-guanine (8-oxo-G) is one of the major sources of spontaneous mutagenesis. Nucleotide-sanitizing enzymes, such as the MutT homolog-1 (MTH1) and nudix-type motif 5 (NUDT5), selectively remove 8-oxo-G from the cellular pool of nucleotides. Previous studies showed that, although the syn conformation generally predominates in purine nucleotides with a bulky substituent at the 8-position, 8-oxo-dGMP binds to both MTH1 and NUDT5 in the anti conformation. This study was initiated to investigate the possibility that 8-oxo-dGMP itself may adopt the anti conformation. Molecular dynamics simulations of mononucleotides (dGMP, 8-oxo-dGMP) in aqueous solution were performed. 8-oxo-dGMP adopted the anti conformation as well as the syn conformation, and the proportion of adopting the anti conformation increased in the presence of metal ions. When 8-oxo-dGMP was in the anti conformation, a metal ion was located between the oxygen atom of phosphate and the oxygen atom at the 8-position of 8-oxo-G. The types of stable anti conformations of 8-oxo-dGMP differed, depending on the ionic radii and charges of coexisting ions. These data suggested a role for metal ions, other than as cofactors for the hydrolysis of the di- and tri-phosphate forms of mononucleotides; that the metal ions help retain the anti conformation of the N-glycosidic torsion angle of 8-oxo-dGMP to promote the binding between the 8-oxo-G deoxynucleotide and the nucleotide-sanitizing enzymes.
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Affiliation(s)
- Shin-Ichi Fujiwara
- Department of Biological Regulation, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago 683-8503, Japan.
| | - Kenichiro Sawada
- Department of Biological Regulation, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago 683-8503, Japan
| | - Takashi Amisaki
- Department of Biological Regulation, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago 683-8503, Japan
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El-Sayed AA, Tamara Molina A, Álvarez-Ros M, Alcolea Palafox M. Conformational analysis of the anti-HIV Nikavir prodrug: comparisons with AZT and Thymidine, and establishment of structure–activity relationships/tendencies in other 6′-derivatives. J Biomol Struct Dyn 2014; 33:723-48. [DOI: 10.1080/07391102.2014.909743] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - A. Tamara Molina
- Facultad de Ciencias Químicas, Departamento de Química-Física I, Universidad Complutense, Ciudad Universitaria, Madrid 28040, Spain
| | - M.C. Álvarez-Ros
- Facultad de Ciencias Químicas, Departamento de Química-Física I, Universidad Complutense, Ciudad Universitaria, Madrid 28040, Spain
| | - M. Alcolea Palafox
- Facultad de Ciencias Químicas, Departamento de Química-Física I, Universidad Complutense, Ciudad Universitaria, Madrid 28040, Spain
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Navarro-Whyte L, Kellie JL, Lenz SAP, Wetmore SD. Hydrolysis of the damaged deoxythymidine glycol nucleoside and comparison to canonical DNA. Phys Chem Chem Phys 2013; 15:19343-52. [DOI: 10.1039/c3cp53217h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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