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dc.contributor.authorGhafoor, Naeem Abdul
dc.contributor.authorSilme, Ragıp Soner
dc.contributor.authorBaysal, Ömür
dc.date.accessioned2021-12-10T11:14:33Z
dc.date.available2021-12-10T11:14:33Z
dc.identifier.citationBaysal Ö., Ghafoor N. A. , Silme R. S. , "Molecular dynamics analysis of N-acetyl-D-glucosamine against specific SARS-CoV-2's pathogenicity factors", Diğer, ss.1-18, 2021
dc.identifier.otherav_71096add-9fae-4a1e-94f4-8795dd2986bb
dc.identifier.othervv_1032021
dc.identifier.urihttp://hdl.handle.net/20.500.12627/171500
dc.identifier.urihttps://avesis.istanbul.edu.tr/api/publication/71096add-9fae-4a1e-94f4-8795dd2986bb/file
dc.description.abstractBackground:The causative agent of virus disease outbreak in the world identified as SARS-CoV-2 leads to a severe respiratory illness similar to that of SARS and MERS. The pathogen outbreak was declared as a pandemic and by the time of this article, it has claimed 2.19 million lives. Computational biology research has provided a lot of insight into many of the structural and functional proteins of the virus and the efforts continue.Methods:We performed molecular docking of several SARS-CoV-2 proteins that are responsible for its pathogenicity against N-acetyl-D-glucosamine via AutoDock Vina and further analyzed the docked poses with molecular dynamics, we also performed a similar experiment for both SARS-CoV-2 and anti-Staphylococcus aureusneutralizing antibodies to establish the potential N-acetyl-D-glucosamine hold in inducing the immune system against the virus.Results:Our new molecular docking and molecular dynamic analysis results have confirmed that SARS-CoV-2 spike receptor-binding domain (PDB: 6M0J), crystal structure of RNA-binding domain of nucleocapsid phosphoprotein from SARS-CoV-2 monoclinic crystal form (PDB: 6WKP), electron microscopy structure of refusion SARS-CoV-2 S ectodomain trimer covalently stabilized in the closed conformation (PDB: 6X79), and X-ray diffraction structure of SARS-CoV-2 main protease 3clpro at room temperature (damage-free XFEL monoclinic, PDB: 7JVZ), and N-acetyl-D-glucosamine could bind on these proteins that play an important role in SARS-CoV-2’s infection. Moreover, our molecular docking analysis data support a strong protein-ligand interaction of N-acetyl-D-glucosamine. These results were confirmed with molecular dynamics studies and the conformational modeling could be used to predict the possible protein-ligand interactions. Additionally, docking analysis against the D614G mutant of the virus have shown that N-acetyl-D-glucosamine affinity was not affected by mutations in the virus’ receptor binding domain. Furthermore, our analysis on the affinity of D-GlcNAc towards human antibodies has shown that it could potentially bind to both SARS-CoV-2 proteins and antibodies hence further induce the immune system against the viral infection.Conclusion:Based on our predictive modelling work, N-acetyl-D-glucosamine holds the potential to inhibit several SARS-CoV-2 proteins as well as induce an immune response against the virus in host system.
dc.language.isoeng
dc.subjectMikrobiyal Genetik
dc.subjectProtein Mühendisliği
dc.subjectTemel Bilimler
dc.subjectMultidisciplinary
dc.subjectCell Biology
dc.subjectDevelopmental Biology
dc.subjectImmunology and Microbiology (miscellaneous)
dc.subjectMolecular Biology
dc.subjectBiotechnology
dc.subjectApplied Microbiology and Biotechnology
dc.subjectMolecular Medicine
dc.subjectVirology
dc.subjectMicrobiology
dc.subjectFamily Practice
dc.subjectMicrobiology (medical)
dc.subjectFundamentals and Skills
dc.subjectGeneral Health Professions
dc.subjectPathophysiology
dc.subjectEmbryology
dc.subjectInternal Medicine
dc.subjectAssessment and Diagnosis
dc.subjectMedicine (miscellaneous)
dc.subjectGeneral Medicine
dc.subjectLife Sciences
dc.subjectHealth Sciences
dc.subjectKlinik Tıp
dc.subjectDoğa Bilimleri Genel
dc.subjectBiyoloji ve Biyokimya
dc.subjectİmmünoloji
dc.subjectMoleküler Biyoloji ve Genetik
dc.subjectMikrobiyoloji
dc.subjectTIP, GENEL & İÇECEK
dc.subjectÇOK DİSİPLİNLİ BİLİMLER
dc.subjectMATEMATİKSEL VE ​​BİLGİSAYAR BİYOLOJİSİ
dc.subjectVİROLOJİ
dc.subjectGELİŞİMSEL BİYOLOJİ
dc.subjectHÜCRE BİYOLOJİSİ
dc.subjectBİYOTEKNOLOJİ VE UYGULAMALI MİKROBİYOLOJİ
dc.subjectMİKROBİYOLOJİ
dc.subjectTıp
dc.subjectSağlık Bilimleri
dc.subjectMikrobiyoloji ve Klinik Mikrobiyoloji
dc.subjectTemel Tıp Bilimleri
dc.subjectKlinik Tıp (MED)
dc.subjectTemel Bilimler (SCI)
dc.subjectYaşam Bilimleri (LIFE)
dc.subjectViroloji
dc.subjectYaşam Bilimleri
dc.subjectBiyoinformatik
dc.subjectBiyoenformasyon
dc.subjectBiyolojik Modelleme
dc.subjectBiyolojik Veritabanları
dc.subjectDiğer
dc.subjectBiyoteknoloji
dc.subjectMoleküler Biyoloji ve Genetik
dc.subjectGenomiks
dc.titleMolecular dynamics analysis of N-acetyl-D-glucosamine against specific SARS-CoV-2's pathogenicity factors
dc.typeDiğer Yayınlar
dc.contributor.departmentMuğla Sıtkı Koçman Üniversitesi , Fen Fakültesi , Moleküler Biyoloji Ve Genetik Bölümü
dc.contributor.firstauthorID2532974


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