Molecular modelling and compound activity of the escherichia coli and staphylococcus aureus DNA gyrase B ATPase site

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dc.authorid0000-0001-6047-2796
dc.authorid0000-0002-2289-7950
dc.authorid0000-0003-1896-2729
dc.contributor.authorBerk, Barkın
dc.contributor.authorKaynar, Gürmen
dc.contributor.authorErtaş, Merve
dc.contributor.authorBiltekin, Sevda Nur
dc.date.accessioned10.07.201910:49:13
dc.date.accessioned2019-07-10T19:36:14Z
dc.date.available10.07.201910:49:14
dc.date.available2019-07-10T19:36:14Z
dc.date.issued2017
dc.departmentİstanbul Medipol Üniversitesi, Eczacılık Fakültesi, Eczacılık Meslek Bilimleri Bölümü, Farmasötik Kimya Ana Bilim Dalı
dc.description.abstractDevelopment of new treatment ligands that can distinguish Escherichia coli (E. coli) from Staphylococcus aureus (S. aureus) is important because of bacterium multiple drug resistance. High-throughput virtual screening (HTVS), docking-scoring and receiver operating characteristic curves are essential components of computational methods used in designing potential new ligands. Here, we investigated the E. coli and S. aureus DNA gyrase B active site; amino acid, water molecule, and ligand interactions using crystallographic data and HTVS to determine potential hits. Trial and test sets were prepared from the 5000 and 50000 compounds of the ZINC databases with known E. coli and S. aureus DNA gyrase B ATPase inhibitor molecules. Trial sets were evaluated and screened by determining the contribution of water molecules to interactions. Data analysis led to the identification of novel interaction patterns, which were screened over a test set; 20 maximum scored compounds were identified and further tested against the novobiocin standard with gel-based E. coli and S. aureus supercoiling assays. The highest scoring N’-(1-naphthylcarbonyl)-2, 1, 3-benzothi-adiazole-5-carbohydrazide structure showed selective inhibition with E. coli and S. aureus DNA gyrase B ATPases. We determined that in terms of selectivity, some water molecules have a major impact on amino acid-ligand interactions.
dc.identifier.citationBerk, B., Kaynar, G., Ertaş, M. ve Biltekin, S.N. (2017). Molecular modelling and compound activity of the escherichia coli and staphylococcus aureus DNA gyrase B ATPase site. Acta Pharmaceutica Sciencia, 55(1), 97-117. https://dx.doi.org/10.23893/1307-2080.APS.0557
dc.identifier.doi10.23893/1307-2080.APS.0557
dc.identifier.endpage117
dc.identifier.issn1307-2080
dc.identifier.issue1
dc.identifier.scopusqualityQ4
dc.identifier.startpage97
dc.identifier.urihttps://hdl.handle.net/20.500.12511/1105
dc.identifier.urihttps://dx.doi.org/10.23893/1307-2080.APS.0557
dc.identifier.volume55
dc.indekslendigikaynakScopus
dc.language.isoen
dc.publisherUniversity of Istanbul
dc.relation.ispartofActa Pharmaceutica Scienciaen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectDNA Gyrase B ATPase
dc.subjectDocking
dc.subjectEscherichia Coli
dc.subjectHTVS
dc.subjectROC Curves
dc.subjectStaphylococcus Aureus
dc.titleMolecular modelling and compound activity of the escherichia coli and staphylococcus aureus DNA gyrase B ATPase site
dc.typeArticle

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