Deciphering the mechanism and binding interactions of Pemetrexed with dsDNA with DNA-targeted chemotherapeutics via spectroscopic, analytical, and simulation studies

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dc.contributor.authorŞenel, Pelin
dc.contributor.authorAgar, Soykan
dc.contributor.authorİş, Yusuf Serhat
dc.contributor.authorAltay, Filiz
dc.contributor.authorGölcü, Ayşegül
dc.contributor.authorYurtsever, Mine
dc.date.accessioned2024-06-13T20:18:02Z
dc.date.available2024-06-13T20:18:02Z
dc.date.issued2022
dc.departmentMeslek Yüksekokulu, Gedik Meslek Yüksekokulu, Kimya Teknolojisi Programı
dc.description.abstractPemetrexed is a well-known and widely used antineoplastic drug under the category of cytotoxic, folate anti-metabolites that is used in chemotherapeutic treatments, especially in malignant mesothelioma and non-small cell lung carcinoma. Here, the binding mechanism and interactions of Pemetrexed with double strain fish sperm deoxyribonucleic acid (dsDNA) were studied thoroughly both experimentally and theoretically, using multi-spectroscopic techniques and molecular docking simulations. Our ultimate goal is to understand better the potential of such antineoplastic drugs and, hence, to design drugs with high dsDNA binding affinities and fewer adverse effects. We employed several techniques yielding different but complementary results such as UV, fluorescence, thermal denaturation, electrochemical and viscosity, and molecular docking studies under physiological conditions. Our results revealed that the Pemetrexed binds fairly strongly to dsDNA's minor groove through hydrogen bond interactions with the mostly adenine and guanine bases via its p-carbamide and p-carboxylic groups. MD simulations of the drug-dsDNA complex were followed for 50 ns to confirm that interaction is stable and robust electrostatic interactions were due to hydrogen bonding mostly with the adenine and guanine nucleotides in the minor groove.
dc.description.sponsorshipIstanbul Technical University [TDK-2020-42630]
dc.identifier.doi10.1016/j.jpba.2021.114490
dc.identifier.issn0731-7085
dc.identifier.issn1873-264X
dc.identifier.pmid34875572
dc.identifier.scopus2-s2.0-85120484389
dc.identifier.scopusqualityQ2
dc.identifier.urihttps://doi.org/10.1016/j.jpba.2021.114490
dc.identifier.urihttps://hdl.handle.net/11501/1183
dc.identifier.volume209
dc.identifier.wosWOS:000734862500006
dc.identifier.wosqualityQ1
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.institutionauthorİş, Yusuf Serhat
dc.institutionauthorid0000-0003-3818-6923
dc.language.isoen
dc.publisherElsevier
dc.relation.ispartofJournal of Pharmaceutical and Biomedical Analysis
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/closedAccess
dc.subjectAntineoplastic Drugs
dc.subjectPemetrexed
dc.subjectdsDNA
dc.subjectSpectroscopy
dc.subjectMolecular Docking
dc.titleDeciphering the mechanism and binding interactions of Pemetrexed with dsDNA with DNA-targeted chemotherapeutics via spectroscopic, analytical, and simulation studies
dc.typeArticle

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