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dc.contributor.authorBelinskaia, D. A.
dc.contributor.authorAvdonin, P. V.
dc.contributor.authorAvdonin, P. P.
dc.contributor.authorJenkins, R. O.
dc.contributor.authorGoncharov, Nikolay V.
dc.date.accessioned2019-06-05T13:45:34Z
dc.date.available2019-06-05T13:45:34Z
dc.date.issued2019-05-13
dc.identifier.citationBelinskaia, D.A., Avdonin, P.V., Jenkins, R.O. and Goncharov, N.V. (2019) Rational in silico design of aptamers for organophosphates based on the example of paraoxon. Computation Biology and Chemistry, 80, pp.452-462.en
dc.identifier.issn1476-9271
dc.identifier.urihttps://www.dora.dmu.ac.uk/handle/2086/17940
dc.descriptionThe file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.en
dc.description.abstractPoisoning by organophosphates (OPs) takes one of the leading places in the total number of exotoxicoses. Detoxication of OPs at the first stage of the poison entering the body could be achieved with the help of DNA- or RNA-aptamers, which are able to bind poisons in the bloodstream. The aim of the research was to develop an approach to rational in silico design of aptamers for OPs based on the example of paraoxon. From the published sequence of an aptamer binding organophosphorus pesticides, its threedimensional model has been constructed. The most probable binding site for paraoxon was determined by molecular docking and molecular dynamics (MD) methods. Then the nucleotides of the binding site were mutated consequently and the values of free binding energy have been calculated using MD trajectories and MM-PBSA approach. On the basis of the energy values, two sequences that bind paraoxon most efficiently have been selected. The value of free binding energy of paraoxon with peripheral anionic site of acetylcholinesterase (AChE) has been calculated as well. It has been revealed that the aptamers found bind paraoxon more effectively than AChE. The peculiarities of paraoxon interaction with the aptamers nucleotides have been analyzed. The possibility of improving in silico approach for aptamer selection is discussed.en
dc.language.isoenen
dc.publisherElsevieren
dc.subjectAptameren
dc.subjectMolecular dockingen
dc.subjectMolecular dynamicsen
dc.subjectRational designen
dc.subjectOrganophosphatesen
dc.titleRational in silico design of aptamers for organophosphates based on the example of paraoxonen
dc.typeArticleen
dc.identifier.doihttps://doi.org/10.1016/j.compbiolchem.2019.05.004
dc.peerreviewedYesen
dc.funderNo external funderen
dc.cclicenceCC BYen
dc.date.acceptance2019-05-08
dc.researchinstituteInstitute for Allied Health Sciences Researchen


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