Molecular structure differences between the antiviral Nucleoside Analogue 5-iodo-2′-deoxyuridine and the natural nucleoside 2′-deoxythymidine using MP2 and DFT methods: conformational analysis, crystal simulations, DNA pairs and possible behaviour

doi:10.1080/07391102.2013.789402

Paper

Molecular structure differences between the antiviral Nucleoside Analogue 5-iodo-2′-deoxyuridine and the natural nucleoside 2′-deoxythymidine using MP2 and DFT methods: conformational analysis, crystal simulations, DNA pairs and possible behaviour

Published Feb 20, 2014 · M. Palafox

Journal of Biomolecular Structure & Dynamics

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Abstract

5-iodo-2'-deoxyuridine Nucleoside Analogue (IUdR) was the first selective antiviral nucleoside against herpes simplex virus type 1 and 2, and it was also a meaningful anticancer drug. Within a full study of this drug and its possible behaviour, previously, a comprehensive theoretical conformational analysis by MP2 and B3LYP was carried out, and all the possible stable structures were determined with full relaxation of all geometrical parameters. The search located 45 stable structures, and in all them, the whole conformational parameters ([Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], P, [Formula: see text]max) were analyzed as well as the NBO natural atomic charges. Comparisons of the conformers with those of the natural Nucleoside 2'-deoxythymidine (dT) were carried out, and the main differences between IUdR and dT were analyzed. The accuracy of the methods used was probed with the simulation of the X-ray crystal data by a tetramer form. Watson-Crick (WC) IUdR/dT···2'-deoxyadenosine pairs were analyzed for the first time using quantum chemical calculations, as well as the mispairing IUdR/dT···2'-deoxyguanosine. As result, it is observed that IUdR give rises to a slightly stronger WC pair and weaker mispairing than those with dT, therefore deforming slightly the DNA axis and difficulting the growth of the DNA virus and consequently, killing it.

Study Snapshot

The antiviral nucleoside analogue 5-iodo-2′-deoxyuridine (IUdR) has slightly stronger Watson-Crick pairs and weaker mispairing than natural nucleoside 2′-deoxythymidine, potentially deforming the DNA axis and hindering virus

PopulationOlder adults (50-71 years)

Sample size24

MethodsObservational

OutcomesBody Mass Index projections

ResultsSocial networks mitigate obesity in older groups.

Molecular structure differences between the antiviral Nucleoside Analogue 5-iodo-2′-deoxyuridine and the natural nucleoside 2′-deoxythymidine using MP2 and DFT methods: conformational analysis, crystal simulations, DNA pairs and possible behaviour

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