In silico identification of SARS-CoV-2 cell entry inhibitors from selected natural antivirals
| العنوان: | In silico identification of SARS-CoV-2 cell entry inhibitors from selected natural antivirals |
|---|---|
| المؤلفون: | Sahra Setenay Baran, Belma Aslim, Yusuf Şimşek |
| المصدر: | Journal of Molecular Graphics & Modelling |
| سنة النشر: | 2021 |
| مصطلحات موضوعية: | In silico, Protein Data Bank (RCSB PDB), ACE2, Molecular Dynamics Simulation, Spike protein, Antiviral Agents, Article, Virus, Neuropilin 1, Materials Chemistry, Neuropilin, Humans, Physical and Theoretical Chemistry, Receptor, Spectroscopy, chemistry.chemical_classification, SARS-CoV-2, COVID-19, Virus Internalization, Antivirals, Computer Graphics and Computer-Aided Design, carbohydrates (lipids), Enzyme, Biochemistry, chemistry, Docking (molecular), Spike Glycoprotein, Coronavirus, Molecular docking |
| الوصف: | The aim of this study is to identify potential drug-like molecules against SARS-CoV-2 virus among the natural antiviral compounds published in the Encyclopedia of Traditional Chinese Medicine. To test inhibition capability of these compounds first, we docked them with Spike protein, angiotensin-converting enzyme 2 (ACE2) (PDB ID: 6M0J) and neuropilin 1 (NRP1) (PDB ID: 7JJC) receptors, and found significant docking scores with extra precision up to −11 kcal/mol. Then, their stability in the binding pockets were further evaluated with molecular dynamics simulation. Eight natural antiviral compounds were identified as potential inhibitors against SARS-CoV-2 cell entry after 200 ns molecular dynamics simulations. We found CMP-3, CMP-4, CMP-5, CMP-6 and CMP-8 are strong binders for the spike protein, CMP-1, CMP-2, CMP-4, CMP-5 and CMP-7 are strong binders for the neuropilin receptor, and CMP-5 is a strong binder for the ACE2. Quercetin derivatives (CMP-4, CMP-5, CMP-6 and CMP-7) were found highly stable in the active domain of NRP1, ACE2 and Spike protein. Especially, CMP-5 showed an inhibitory activity for all targets. These natural antivirals may be potential drug candidates for the prevention of SARS-CoV-2 infection. Graphical abstract Image 1 |
| اللغة: | English |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::73019a2e9847b3a71918661361246757Test https://avesis.gazi.edu.tr/publication/details/458fa333-3659-49af-8482-892f25c5eff4/oaiTest |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....73019a2e9847b3a71918661361246757 |
| قاعدة البيانات: | OpenAIRE |
| الوصف غير متاح. |