Docking and molecular dynamics calculations of some previously studied and newly designed ligands to catalytic core domain of HIV-1 integrase and an investigation to effects of conformational changes of protein on docking results

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dc.authorid0000-0002-9528-6122en_US
dc.contributor.authorErcan, Selami
dc.date.accessioned2019-05-23T11:01:33Z
dc.date.available2019-05-23T11:01:33Z
dc.date.issued2017-01-09
dc.departmentBatman Üniversitesi Sağlık Yüksekokulu Hemşirelik Bölümüen_US
dc.description.abstractNowadays, AIDS still remains as a worldwide pandemic and continues to cause many deaths which arise from HIV-1 virus. For nearly 35 years, drugs that target various steps of virus life cycle have been developed. HIV-1 integrase constitutes one of these steps which is essential for virus life cycle. Computer-aided drug design is being used in many drug development and drug improvement studies as also used in development of the first HIV-1 integrase inhibitor Raltegravir. In this study, 3 ligands which are already used as HIV-1 integrase inhibitors and 4 newly designed ligands were docked to catalytic core domain of HIV-1 integrase. Each ligand docked to three different conformations of protein. Prepared complexes (21 items) were carried out by 50 ns MD simulations and results were analyzed. Finally, the binding free energies of ligands were calculated. It was determined that designed ligands L01 and L03 gave favorable results. The questions about the ligands which have low docking scores in a conformation of protein could give better scores in another conformation of protein and if the MD simulations carry the different oriented and different localized ligands in same position at the end of simulation were answered.en_US
dc.identifier.citationErcan, S. (2017). Docking and molecular dynamics calculations of some previously studied and newly designed ligands to catalytic core domain of HIV-1 integrase and an investigation to effects of conformational changes of protein on docking results. Journal of the Turkish Chemical Society, Section A: Chemistry, 4 (1), pp. 243-270. https://doi.org/10.18596/jotcsa.287327en_US
dc.identifier.endpage270en_US
dc.identifier.issn2149-0120
dc.identifier.issue1en_US
dc.identifier.scopusqualityQ4en_US
dc.identifier.startpage243en_US
dc.identifier.urihttps://hdl.handle.net/20.500.12402/2033
dc.identifier.volume4en_US
dc.identifier.wosqualityN/Aen_US
dc.indekslendigikaynakTR-Dizinen_US
dc.language.isoenen_US
dc.publisherTürkiye Kimya Derneğien_US
dc.relation.isversionof10.18596/jotcsa.287327en_US
dc.relation.journalJournal of the Turkish Chemical Society, Section A: Chemistryen_US
dc.relation.publicationcategoryMakale - Ulusal Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.rightsAttribution-NonCommercial-ShareAlike 3.0 United States*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/3.0/us/*
dc.subjectHIV-1 Integraseen_US
dc.subjectDrug Designen_US
dc.subjectDockingen_US
dc.subjectMolecular Dynamicsen_US
dc.subjectBinding Free Energyen_US
dc.titleDocking and molecular dynamics calculations of some previously studied and newly designed ligands to catalytic core domain of HIV-1 integrase and an investigation to effects of conformational changes of protein on docking resultsen_US
dc.typeArticleen_US

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