Molecular Dynamics Simulation of SARS-CoV-2 E Ion Channel : The Study of Lone Protein and its Conformational Changes in Complex with Potential Cage Inhibitors
Copyright© Bentham Science Publishers; For any queries, please email at epubbenthamscience.net..
BACKGROUND: The coronavirus E ion channel has previously been studied as a potential target for antiviral therapy, with several compounds found to bind to the channel. However, these compounds have low activity, searching for effective E ion channel inhibitors of great importance.
OBJECTIVE: This study aimed to develop a computational approach for designing ligands for the coronaviral E ion channel and identify potential inhibitors based on this approach.
METHODS: The structure of the E-ion channel was refined using molecular dynamics, and the pore responsible for binding cage compounds was selected as the inhibitor-binding site. Potential inhibitor structures were identified using molecular docking, and their binding was confirmed using molecular dynamics simulations.
RESULTS: A number of potential SARS E ion channel inhibitors have been identified, and the binding modes and possible mechanisms of action of these inhibitors have been clarified.
CONCLUSION: This study presents a computational approach that can be used to design ligands for E ion channels and identify potential inhibitors, providing valuable insights into the development of new antiviral therapies. The behavior of the E protein pentamer of SARS-CoV-2 in its native environment was investigated using Molecular Dynamics (MD), resulting in an equilibrated structure that could be used to develop new inhibitors through molecular docking. Simulation of the MD of E-channel complexes with amantadine analogues allowed for the identification of the main types of ligand-protein interactions that are responsible for the good binding of ligands within the channel's inner chamber.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2024 |
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| Erschienen: |
2024 |
| Enthalten in: |
Zur Gesamtaufnahme - year:2024 |
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| Enthalten in: |
Current computer-aided drug design - (2024) vom: 05. Apr. |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Shiryaev, Vadim Andreevich [VerfasserIn] |
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| Links: |
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| Themen: |
Adamantanes. |
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| Anmerkungen: |
Date Revised 09.04.2024 published: Print-Electronic Citation Status Publisher |
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| doi: |
10.2174/0115734099247899240326073802 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM370805577 |
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| 100 | 1 | |a Shiryaev, Vadim Andreevich |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Molecular Dynamics Simulation of SARS-CoV-2 E Ion Channel |b The Study of Lone Protein and its Conformational Changes in Complex with Potential Cage Inhibitors |
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| 500 | |a Date Revised 09.04.2024 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status Publisher | ||
| 520 | |a Copyright© Bentham Science Publishers; For any queries, please email at epubbenthamscience.net. | ||
| 520 | |a BACKGROUND: The coronavirus E ion channel has previously been studied as a potential target for antiviral therapy, with several compounds found to bind to the channel. However, these compounds have low activity, searching for effective E ion channel inhibitors of great importance | ||
| 520 | |a OBJECTIVE: This study aimed to develop a computational approach for designing ligands for the coronaviral E ion channel and identify potential inhibitors based on this approach | ||
| 520 | |a METHODS: The structure of the E-ion channel was refined using molecular dynamics, and the pore responsible for binding cage compounds was selected as the inhibitor-binding site. Potential inhibitor structures were identified using molecular docking, and their binding was confirmed using molecular dynamics simulations | ||
| 520 | |a RESULTS: A number of potential SARS E ion channel inhibitors have been identified, and the binding modes and possible mechanisms of action of these inhibitors have been clarified | ||
| 520 | |a CONCLUSION: This study presents a computational approach that can be used to design ligands for E ion channels and identify potential inhibitors, providing valuable insights into the development of new antiviral therapies. The behavior of the E protein pentamer of SARS-CoV-2 in its native environment was investigated using Molecular Dynamics (MD), resulting in an equilibrated structure that could be used to develop new inhibitors through molecular docking. Simulation of the MD of E-channel complexes with amantadine analogues allowed for the identification of the main types of ligand-protein interactions that are responsible for the good binding of ligands within the channel's inner chamber | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Coronavirus | |
| 650 | 4 | |a E ion channel | |
| 650 | 4 | |a adamantanes. | |
| 650 | 4 | |a cage compounds | |
| 650 | 4 | |a molecular docking | |
| 650 | 4 | |a molecular dynamics | |
| 700 | 1 | |a Ivleva, Elena Alexandrovna |e verfasserin |4 aut | |
| 700 | 1 | |a Zaborskaya, Maria Sergeevna |e verfasserin |4 aut | |
| 700 | 1 | |a Tkachenko, Ilya Michailovich |e verfasserin |4 aut | |
| 700 | 1 | |a Osyanin, Vitaly Alexandrovich |e verfasserin |4 aut | |
| 700 | 1 | |a Klimochkin, Yuri Nikolaevich |e verfasserin |4 aut | |
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