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Open AccessArticle

Biomolecules of 2-Thiouracil, 4-Thiouracil and 2,4-Dithiouracil: A DFT Study of the Hydration, Molecular Docking and Effect in DNA:RNAMicrohelixes

1
Departamento de Química-Física, Facultad de CienciasQuímicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
2
PG and Research Department of Physics, N.M.S.S.V.N. College, Madurai 625019, India
3
Indian Spectroscopy Society, KC 68/1, Old Kavinagar, Ghaziabad 201002, India
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(14), 3477; https://doi.org/10.3390/ijms20143477
Received: 24 June 2019 / Revised: 10 July 2019 / Accepted: 11 July 2019 / Published: 15 July 2019
(This article belongs to the Special Issue DFT Applications to Biomolecules and Complex Reactions)
The molecular structure of 2-thiouracil, 4-thiouracil and 2,4-dithiouracil was analyzed under the effect of the first and second hydration shell by using the B3LYP density functional (DFT) method, and the results were compared to those obtained for the uracil molecule. A slight difference in the water distribution appears in these molecules. On the hydration of these molecules several trends in bond lengths and atomic charges were established. The ring in uracil molecule appears easier to be deformed and adapted to different environments as compared to that when it is thio-substituted. Molecular docking calculations of 2-thiouracil against three different pathogens: Bacillus subtilis, Escherichia coli and Candida albicans were carried out. Docking calculations of 2,4-dithiouracil ligand with various targeted proteins were also performed. Different DNA: RNA hybrid microhelixes with uridine, 2-thiouridine, 4-thiouridine and 2,4-dithiouridine nucleosides were optimized in a simple model with three nucleotide base pairs. Two main types of microhelixes were analyzed in detail depending on the intramolecular H-bond of the 2′-OH group. The weaker Watson–Crick (WC) base pair formed with thio-substituted uracil than with unsubstituted ones slightly deforms the helical and backbone parameters, especially with 2,4-dithiouridine. However, the thio-substitution significantly increases the dipole moment of the A-type microhelixes, as well as the rise and propeller twist parameters. View Full-Text
Keywords: thiouracil compounds; hydration; molecular docking; hybrid microhelixes; DNA:RNA thiouracil compounds; hydration; molecular docking; hybrid microhelixes; DNA:RNA
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MDPI and ACS Style

Alcolea Palafox, M.; Franklin Benial, A.M.; K. Rastogi, V. Biomolecules of 2-Thiouracil, 4-Thiouracil and 2,4-Dithiouracil: A DFT Study of the Hydration, Molecular Docking and Effect in DNA:RNAMicrohelixes. Int. J. Mol. Sci. 2019, 20, 3477. https://doi.org/10.3390/ijms20143477

AMA Style

Alcolea Palafox M, Franklin Benial AM, K. Rastogi V. Biomolecules of 2-Thiouracil, 4-Thiouracil and 2,4-Dithiouracil: A DFT Study of the Hydration, Molecular Docking and Effect in DNA:RNAMicrohelixes. International Journal of Molecular Sciences. 2019; 20(14):3477. https://doi.org/10.3390/ijms20143477

Chicago/Turabian Style

Alcolea Palafox, M.; Franklin Benial, A. M.; K. Rastogi, V. 2019. "Biomolecules of 2-Thiouracil, 4-Thiouracil and 2,4-Dithiouracil: A DFT Study of the Hydration, Molecular Docking and Effect in DNA:RNAMicrohelixes" Int. J. Mol. Sci. 20, no. 14: 3477. https://doi.org/10.3390/ijms20143477

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