Oleuropein as a Potent Compound against Neurological Complications Linked with COVID-19: A Computational Biology Approach
The association of COVID-19 with neurological complications is a well-known fact, and researchers are endeavoring to investigate the mechanistic perspectives behind it. SARS-CoV-2 can bind to Toll-like receptor 4 (TLR-4) that would eventually lead to α-synuclein aggregation in neurons and stimulatio...
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| Format: | Article |
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MDPI AG
2022-06-01
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| Online Access: | https://www.mdpi.com/1099-4300/24/7/881 |
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| author | Talib Hussain Alaa Hamed Habib Misbahuddin M. Rafeeq Ahmed Alafnan El-Sayed Khafagy Danish Iqbal Qazi Mohammad Sajid Jamal Rahamat Unissa Dinesh C. Sharma Afrasim Moin Syed Mohd Danish Rizvi |
| author_facet | Talib Hussain Alaa Hamed Habib Misbahuddin M. Rafeeq Ahmed Alafnan El-Sayed Khafagy Danish Iqbal Qazi Mohammad Sajid Jamal Rahamat Unissa Dinesh C. Sharma Afrasim Moin Syed Mohd Danish Rizvi |
| author_sort | Talib Hussain |
| collection | DOAJ |
| description | The association of COVID-19 with neurological complications is a well-known fact, and researchers are endeavoring to investigate the mechanistic perspectives behind it. SARS-CoV-2 can bind to Toll-like receptor 4 (TLR-4) that would eventually lead to α-synuclein aggregation in neurons and stimulation of neurodegeneration pathways. Olive leaves have been reported as a promising phytotherapy or co-therapy against COVID-19, and oleuropein is one of the major active components of olive leaves. In the current study, oleuropein was investigated against SARS-CoV-2 target (main protease 3CL<sup>pro</sup>), TLR-4 and Prolyl Oligopeptidases (POP), to explore oleuropein potency against the neurological complications associated with COVID-19. Docking experiments, docking validation, interaction analysis, and molecular dynamic simulation analysis were performed to provide insight into the binding pattern of oleuropein with the three target proteins. Interaction analysis revealed strong bonding between oleuropein and the active site amino acid residues of the target proteins. Results were further compared with positive control lopinavir (3CL<sup>pro</sup>), resatorvid (TLR-4), and berberine (POP). Moreover, molecular dynamic simulation was performed using YASARA structure tool, and AMBER14 force field was applied to examine an 100 ns trajectory run. For each target protein-oleuropein complex, RMSD, RoG, and total potential energy were estimated, and 400 snapshots were obtained after each 250 ps. Docking analyses showed binding energy as −7.8, −8.3, and −8.5 kcal/mol for oleuropein-3CL<sup>pro</sup>, oleuropein-TLR4, and oleuropein-POP interactions, respectively. Importantly, target protein-oleuropein complexes were stable during the 100 ns simulation run. However, an experimental in vitro study of the binding of oleuropein to the purified targets would be necessary to confirm the present study outcomes. |
| first_indexed | 2024-03-09T10:19:21Z |
| format | Article |
| id | doaj.art-87b2f3bfdca748c58716ec2bbd1103ef |
| institution | Directory Open Access Journal |
| issn | 1099-4300 |
| language | English |
| last_indexed | 2024-03-09T10:19:21Z |
| publishDate | 2022-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Entropy |
| spelling | doaj.art-87b2f3bfdca748c58716ec2bbd1103ef2023-12-01T22:06:35ZengMDPI AGEntropy1099-43002022-06-0124788110.3390/e24070881Oleuropein as a Potent Compound against Neurological Complications Linked with COVID-19: A Computational Biology ApproachTalib Hussain0Alaa Hamed Habib1Misbahuddin M. Rafeeq2Ahmed Alafnan3El-Sayed Khafagy4Danish Iqbal5Qazi Mohammad Sajid Jamal6Rahamat Unissa7Dinesh C. Sharma8Afrasim Moin9Syed Mohd Danish Rizvi10Department of Pharmacology and Toxicology, College of Pharmacy, University of Hail, Hail P.O. Box 2440, Saudi ArabiaDepartment of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi ArabiaDepartment of Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi ArabiaDepartment of Pharmacology and Toxicology, College of Pharmacy, University of Hail, Hail P.O. Box 2440, Saudi ArabiaDepartment of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-kharj 11942, Saudi ArabiaDepartment of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi ArabiaDepartment of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi ArabiaDepartment of Pharmaceutics, College of Pharmacy, University of Hail, Hail P.O. Box 2440, Saudi ArabiaSchool of Life Sciences, The Glocal University, Saharanpur 247121, Uttar Pradesh, IndiaDepartment of Pharmaceutics, College of Pharmacy, University of Hail, Hail P.O. Box 2440, Saudi ArabiaDepartment of Pharmaceutics, College of Pharmacy, University of Hail, Hail P.O. Box 2440, Saudi ArabiaThe association of COVID-19 with neurological complications is a well-known fact, and researchers are endeavoring to investigate the mechanistic perspectives behind it. SARS-CoV-2 can bind to Toll-like receptor 4 (TLR-4) that would eventually lead to α-synuclein aggregation in neurons and stimulation of neurodegeneration pathways. Olive leaves have been reported as a promising phytotherapy or co-therapy against COVID-19, and oleuropein is one of the major active components of olive leaves. In the current study, oleuropein was investigated against SARS-CoV-2 target (main protease 3CL<sup>pro</sup>), TLR-4 and Prolyl Oligopeptidases (POP), to explore oleuropein potency against the neurological complications associated with COVID-19. Docking experiments, docking validation, interaction analysis, and molecular dynamic simulation analysis were performed to provide insight into the binding pattern of oleuropein with the three target proteins. Interaction analysis revealed strong bonding between oleuropein and the active site amino acid residues of the target proteins. Results were further compared with positive control lopinavir (3CL<sup>pro</sup>), resatorvid (TLR-4), and berberine (POP). Moreover, molecular dynamic simulation was performed using YASARA structure tool, and AMBER14 force field was applied to examine an 100 ns trajectory run. For each target protein-oleuropein complex, RMSD, RoG, and total potential energy were estimated, and 400 snapshots were obtained after each 250 ps. Docking analyses showed binding energy as −7.8, −8.3, and −8.5 kcal/mol for oleuropein-3CL<sup>pro</sup>, oleuropein-TLR4, and oleuropein-POP interactions, respectively. Importantly, target protein-oleuropein complexes were stable during the 100 ns simulation run. However, an experimental in vitro study of the binding of oleuropein to the purified targets would be necessary to confirm the present study outcomes.https://www.mdpi.com/1099-4300/24/7/881oleuropeinCOVID-19SARS-CoV-2TLR-43CL<sup>pro</sup>molecular dynamics |
| spellingShingle | Talib Hussain Alaa Hamed Habib Misbahuddin M. Rafeeq Ahmed Alafnan El-Sayed Khafagy Danish Iqbal Qazi Mohammad Sajid Jamal Rahamat Unissa Dinesh C. Sharma Afrasim Moin Syed Mohd Danish Rizvi Oleuropein as a Potent Compound against Neurological Complications Linked with COVID-19: A Computational Biology Approach Entropy oleuropein COVID-19 SARS-CoV-2 TLR-4 3CL<sup>pro</sup> molecular dynamics |
| title | Oleuropein as a Potent Compound against Neurological Complications Linked with COVID-19: A Computational Biology Approach |
| title_full | Oleuropein as a Potent Compound against Neurological Complications Linked with COVID-19: A Computational Biology Approach |
| title_fullStr | Oleuropein as a Potent Compound against Neurological Complications Linked with COVID-19: A Computational Biology Approach |
| title_full_unstemmed | Oleuropein as a Potent Compound against Neurological Complications Linked with COVID-19: A Computational Biology Approach |
| title_short | Oleuropein as a Potent Compound against Neurological Complications Linked with COVID-19: A Computational Biology Approach |
| title_sort | oleuropein as a potent compound against neurological complications linked with covid 19 a computational biology approach |
| topic | oleuropein COVID-19 SARS-CoV-2 TLR-4 3CL<sup>pro</sup> molecular dynamics |
| url | https://www.mdpi.com/1099-4300/24/7/881 |
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