Exploring Therapeutic Potential of Nutraceutical Compounds from Propolis on MAPK1 Protein Using Bioinformatics Approaches as Anti-Coronavirus Disease 2019 (COVID-19)
Khalish Arsy Al Khairy Siregar, Paula Mariana Kustiawan, Anissa Nofita Sari, Feri Eko Hermanto
BIO Web of Conferences, doi:10.1051/bioconf/20248800007
This study explores the potential of propolis, a natural substance, as a gene therapy for treating COVID-19. Despite the advent of COVID-19 vaccines, their side effects pose new health challenges. Utilizing network pharmacology, this research identifies propolis compounds through various databases and assesses their ability to target proteins associated with COVID-19. MAPK1 emerges as a potential therapeutic target, and molecular docking reveals Broussoflavonol F, Glyasperin A, and Sulabiroins as promising compounds with strong binding affinities, i.e., -9.0, -9.0, and -8.8 kcal/mol, respectively, exceeding the native ligand (-7.2 kcal/mol). Molecular Dynamics displays stable complex behavior, with backbone RMSD values consistently below 4 Angstroms and RMSF simulations showing minimal fluctuations within ±2 Angstroms error. Moreover, MM-PBSA analysis further supports the strong binding of Broussoflavonol F, Glyasperin A, and Sulabiroins A, with relative binding energies of -122.82±89.65, 131.48±95.39, and -155.97±111,37 kJ/mol, respectively. These results indicate that propolis has potential as an anti-COVID-19 agent, primarily through inhibiting the MAPK1 pathway. However, further research is needed to validate these results and develop practical applications for COVID-19 therapy. This study underscores the significance of network pharmacology and computational models in understanding propolis mechanisms, offering potential directions for future research and treatment strategies against COVID-19.
Bold : The same amino acids where references drugs and compounds interact with proteins and support from PDB ID literature source.
Molecular Dynamics The potential compound selected as a result of molecular docking is reported to have better interaction stability (RMSD, RMSF, and Binding Energy) than Norathyriol, based on molecular dynamics results. The Root-Mean-Square Deviation (RMSD) value of the backbone structure shows that the MAPK1 complex with Sulabiroins A has better stability than the Native Ligand. Similarly, RMSD of the ligand structure also confirmed that Sulalabiroins A had better structural stability than Native Ligand. The average RMSF values obtained for Norathyriol (Control), Broussoflavonol F, Glyasperin A and Sulabiroins A were 1.51 Å, 1.65 Å and 1.48 Å respectively, indicating relatively stable behavior. The stability of the Active Sites distributed in each complex is reported to confirm the Complex Docking and Conformation results obtained from dynamic simulations. Based on the structural arrangement of the MAPK1 complex and its interactions with the active site residues of several selected compounds, it shows consistent stability below 2 Å during the simulation. Based on a comprehensive analysis of root mean square fluctuations (RMSF), it can be concluded that no statistically significant fluctuations were observed in the investigated system. Thus, the results of binding energy calculations found that Sulabiroins A, Glyasperin A and Broussoflavonol F..
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'abstract': '<jats:p>This study explores the potential of propolis, a natural substance, as a gene therapy '
'for treating COVID-19. Despite the advent of COVID-19 vaccines, their side effects pose new '
'health challenges. Utilizing network pharmacology, this research identifies propolis '
'compounds through various databases and assesses their ability to target proteins associated '
'with COVID-19. MAPK1 emerges as a potential therapeutic target, and molecular docking reveals '
'Broussoflavonol F, Glyasperin A, and Sulabiroins as promising compounds with strong binding '
'affinities, i.e.,- 9.0, -9.0, and -8.8 kcal/mol, respectively, exceeding the native ligand '
'(-7.2 kcal/mol). Molecular Dynamics displays stable complex behavior, with backbone RMSD '
'values consistently below 4 Angstroms and RMSF simulations showing minimal fluctuations '
'within ±2 Angstroms error. Moreover, MM-PBSA analysis further supports the strong binding of '
'Broussoflavonol F, Glyasperin A, and Sulabiroins A, with relative binding energies of '
'-122.82±89.65, 131.48±95.39, and -155.97±111,37 kJ/mol, respectively. These results indicate '
'that propolis has potential as an anti-COVID-19 agent, primarily through inhibiting the MAPK1 '
'pathway. However, further research is needed to validate these results and develop practical '
'applications for COVID-19 therapy. This study underscores the significance of network '
'pharmacology and computational models in understanding propolis mechanisms, offering '
'potential directions for future research and treatment strategies against COVID-19.</jats:p>',
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