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

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dc.contributor.authorAlcolea Palafox, Mauricio
dc.contributor.authorFranklin Benial, A. Milton
dc.contributor.authorK. Rastogi, V.
dc.date.accessioned2023-06-17T12:36:23Z
dc.date.available2023-06-17T12:36:23Z
dc.date.issued2019-07-15
dc.description.abstractThe 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.
dc.description.departmentDepto. de Química Física
dc.description.facultyFac. de Ciencias Químicas
dc.description.refereedTRUE
dc.description.statuspub
dc.eprint.idhttps://eprints.ucm.es/id/eprint/66280
dc.identifier.doi10.3390/ijms20143477
dc.identifier.issn1422-0067
dc.identifier.officialurlhttps://doi.org/10.3390/ijms20143477
dc.identifier.relatedurlhttps://www.mdpi.com/1422-0067/20/14/3477
dc.identifier.urihttps://hdl.handle.net/20.500.14352/12605
dc.issue.number14
dc.journal.titleInternational Journal of Molecular Sciences
dc.language.isoeng
dc.page.initial3477
dc.publisherMDPI
dc.rightsAtribución 3.0 España
dc.rights.accessRightsopen access
dc.rights.urihttps://creativecommons.org/licenses/by/3.0/es/
dc.subject.keywordthiouracil compounds
dc.subject.keywordhydration
dc.subject.keywordmolecular docking
dc.subject.keywordhybrid microhelixes
dc.subject.keywordDNA:RNA
dc.subject.ucmQuímica física (Química)
dc.titleBiomolecules of 2-Thiouracil, 4-Thiouracil and 2,4-Dithiouracil: A DFT Study of the Hydration, Molecular Docking and Effect in DNA:RNAMicrohelixes
dc.typejournal article
dc.volume.number20
dspace.entity.typePublication
relation.isAuthorOfPublication1163c7a4-e779-417f-867c-a6e963e4525e
relation.isAuthorOfPublication.latestForDiscovery1163c7a4-e779-417f-867c-a6e963e4525e
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