Phytochemicals from Leucas zeylanica Targeting Main Protease of SARS-CoV-2 : Chemical Profiles, Molecular Docking, and Molecular Dynamics Simulations
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a contemporary coronavirus, has impacted global economic activity and has a high transmission rate. As a result of the virus's severe medical effects, developing effective vaccinations is vital. Plant-derived metabolites have been discovered as potential SARS-CoV-2 inhibitors. The SARS-CoV-2 main protease (Mpro) is a target for therapeutic research because of its highly conserved protein sequence. Gas chromatography-mass spectrometry (GC-MS) and molecular docking were used to screen 34 compounds identified from Leucas zeylanica for potential inhibitory activity against the SARS-CoV-2 Mpro. In addition, prime molecular mechanics-generalized Born surface area (MM-GBSA) was used to screen the compound dataset using a molecular dynamics simulation. From molecular docking analysis, 26 compounds were capable of interaction with the SARS-CoV-2 Mpro, while three compounds, namely 11-oxa-dispiro[4.0.4.1]undecan-1-ol (-5.755 kcal/mol), azetidin-2-one 3,3-dimethyl-4-(1-aminoethyl) (-5.39 kcal/mol), and lorazepam, 2TMS derivative (-5.246 kcal/mol), exhibited the highest docking scores. These three ligands were assessed by MM-GBSA, which revealed that they bind with the necessary Mpro amino acids in the catalytic groove to cause protein inhibition, including Ser144, Cys145, and His41. The molecular dynamics simulation confirmed the complex rigidity and stability of the docked ligand-Mpro complexes based on the analysis of mean radical variations, root-mean-square fluctuations, solvent-accessible surface area, radius of gyration, and hydrogen bond formation. The study of the postmolecular dynamics confirmation also confirmed that lorazepam, 11-oxa-dispiro[4.0.4.1]undecan-1-ol, and azetidin-2-one-3, 3-dimethyl-4-(1-aminoethyl) interact with similar Mpro binding pockets. The results of our computerized drug design approach may assist in the fight against SARS-CoV-2.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:10 |
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| Enthalten in: |
Biology - 10(2021), 8 vom: 17. Aug. |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Dutta, Mycal [VerfasserIn] |
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| Links: |
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| Themen: |
COVID-19 |
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| Anmerkungen: |
Date Revised 07.11.2023 published: Electronic Citation Status PubMed-not-MEDLINE |
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| doi: |
10.3390/biology10080789 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| 245 | 1 | 0 | |a Phytochemicals from Leucas zeylanica Targeting Main Protease of SARS-CoV-2 |b Chemical Profiles, Molecular Docking, and Molecular Dynamics Simulations |
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| 520 | |a Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a contemporary coronavirus, has impacted global economic activity and has a high transmission rate. As a result of the virus's severe medical effects, developing effective vaccinations is vital. Plant-derived metabolites have been discovered as potential SARS-CoV-2 inhibitors. The SARS-CoV-2 main protease (Mpro) is a target for therapeutic research because of its highly conserved protein sequence. Gas chromatography-mass spectrometry (GC-MS) and molecular docking were used to screen 34 compounds identified from Leucas zeylanica for potential inhibitory activity against the SARS-CoV-2 Mpro. In addition, prime molecular mechanics-generalized Born surface area (MM-GBSA) was used to screen the compound dataset using a molecular dynamics simulation. From molecular docking analysis, 26 compounds were capable of interaction with the SARS-CoV-2 Mpro, while three compounds, namely 11-oxa-dispiro[4.0.4.1]undecan-1-ol (-5.755 kcal/mol), azetidin-2-one 3,3-dimethyl-4-(1-aminoethyl) (-5.39 kcal/mol), and lorazepam, 2TMS derivative (-5.246 kcal/mol), exhibited the highest docking scores. These three ligands were assessed by MM-GBSA, which revealed that they bind with the necessary Mpro amino acids in the catalytic groove to cause protein inhibition, including Ser144, Cys145, and His41. The molecular dynamics simulation confirmed the complex rigidity and stability of the docked ligand-Mpro complexes based on the analysis of mean radical variations, root-mean-square fluctuations, solvent-accessible surface area, radius of gyration, and hydrogen bond formation. The study of the postmolecular dynamics confirmation also confirmed that lorazepam, 11-oxa-dispiro[4.0.4.1]undecan-1-ol, and azetidin-2-one-3, 3-dimethyl-4-(1-aminoethyl) interact with similar Mpro binding pockets. The results of our computerized drug design approach may assist in the fight against SARS-CoV-2 | ||
| 650 | 4 | |a Journal Article | |
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| 650 | 4 | |a GC-MS | |
| 650 | 4 | |a Leucas zeylanica | |
| 650 | 4 | |a SARS-CoV-2 | |
| 650 | 4 | |a main protease | |
| 650 | 4 | |a molecular dynamics simulation | |
| 700 | 1 | |a Tareq, Abu Montakim |e verfasserin |4 aut | |
| 700 | 1 | |a Rakib, Ahmed |e verfasserin |4 aut | |
| 700 | 1 | |a Mahmud, Shafi |e verfasserin |4 aut | |
| 700 | 1 | |a Sami, Saad Ahmed |e verfasserin |4 aut | |
| 700 | 1 | |a Mallick, Jewel |e verfasserin |4 aut | |
| 700 | 1 | |a Islam, Mohammad Nazmul |e verfasserin |4 aut | |
| 700 | 1 | |a Majumder, Mohuya |e verfasserin |4 aut | |
| 700 | 1 | |a Uddin, Md Zia |e verfasserin |4 aut | |
| 700 | 1 | |a Alsubaie, Abdullah |e verfasserin |4 aut | |
| 700 | 1 | |a Almalki, Abdulraheem S A |e verfasserin |4 aut | |
| 700 | 1 | |a Khandaker, Mayeen Uddin |e verfasserin |4 aut | |
| 700 | 1 | |a Bradley, D A |e verfasserin |4 aut | |
| 700 | 1 | |a Rana, Md Sohel |e verfasserin |4 aut | |
| 700 | 1 | |a Emran, Talha Bin |e verfasserin |4 aut | |
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