Comparative molecular docking analysis of carbapenem antibiotics with NDM-1 and OXA-23 Β-lactamases: Insights into binding mechanisms

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dc.authorid0000-0003-1721-0314
dc.authorid0000-0002-6414-9336
dc.contributor.authorSarıyer, Emrah
dc.contributor.authorAğırbaş, Gamze
dc.date.accessioned2026-07-09T08:41:41Z
dc.date.available2026-07-09T08:41:41Z
dc.date.issued2025
dc.departmentAÇÜ, Sağlık Hizmetleri Meslek Yüksekokulu, Tıbbi Hizmetler ve Teknikler Bölümü
dc.description.abstractObjective: This study aimed to investigate the molecular interactions between carbapenem antibiotics (imipenem and meropenem) and two (3-lactamase enzymes, NDM-1 (class B) and OXA-23 (class D), to understand the structural basis of carbapenem resistance. Methods: The study employed molecular docking methods using the crystal structures and homology models of the NDM-1 and OXA-23 enzymes to analyze binding affinities and interaction patterns. Results: The results revealed distinct binding characteristics for each enzyme. NDM-1 exhibited a polar, hydrophobic active site, with imipenem forming hydrogen bonds with ASP124, ASN220, and LYS211, while meropenem relied on weaker interactions like Van der Waals forces. In contrast, OXA-23 featured a hydrophobic cavity with charged residues, where imipenem bonded with ARG259 and meropenem interacted with SER79, TRP219, and ARG259. A key finding was the significantly lower binding energy for the OXA-23-imipenem complex in the crystal structure (-8.06 kcal/mol) compared to its homology model (-5.34 kcal/mol), highlighting the importance of accurate structural representation. The study demonstrated strong agreement between the computational and experimental data. Conclusion: These findings provide critical insights into the structural basis of carbapenem resistance, offering potential avenues for designing inhibitors to combat (3-lactamase-mediated antibiotic resistance. The integrated approach validates the utility of computational methods in elucidating molecular interactions and guiding therapeutic strategies.
dc.identifier.doi10.33808/clinexphealthsci.1675807
dc.identifier.endpage660
dc.identifier.issn2459-1459
dc.identifier.issue3
dc.identifier.startpage654
dc.identifier.urihttps://hdl.handle.net/11494/6295
dc.identifier.volume15
dc.identifier.wosWOS:001593250700025
dc.identifier.wosqualityQ4
dc.indekslendigikaynakWeb of Science
dc.institutionauthorSarıyer, Emrah
dc.institutionauthorAğırbaş, Gamze
dc.institutionauthorid0000-0003-1721-0314
dc.institutionauthorid0000-0002-6414-9336
dc.language.isoen
dc.publisherMARMARA UNIV
dc.relation.ispartofCLINICAL AND EXPERIMENTAL HEALTH SCIENCES
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectNDM-1
dc.subjectOXA-23
dc.subjectImipenem
dc.subjectMeropenem
dc.subjectMolecular docking
dc.titleComparative molecular docking analysis of carbapenem antibiotics with NDM-1 and OXA-23 Β-lactamases: Insights into binding mechanisms
dc.typeArticle

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