Bioactive Compounds in Citrus reticulata Peel Are Potential Candidates for Alleviating Physical Fatigue through a Triad Approach of Network Pharmacology, Molecular Docking, and Molecular Dynamics Modeling
Abstract
:1. Introduction
2. Materials and Methods
2.1. Establishing Database for Bioactive Compounds of Citrus reticulata Peel
2.2. Identification of Bioactive Compounds of CR-P and Related Targets
2.3. Identification of Physical Fatigue-Related Targets
2.4. Key Overlapping Targets of CR-P and Physical Fatigue
2.5. Network Construction of Protein–Protein Interaction (PPI)
2.6. GO and KEGG Pathway Enrichment Analysis
2.7. Network Construction of Target-Pathway Interaction
2.8. Molecular Docking
2.9. Molecular Dynamics Simulation
3. Results
3.1. Bioactive Compounds of CR-P and Related Targets
3.2. Potential Targets of Physical Fatigue
3.3. Key Overlapping Targets of CR-P and Physical Fatigue
3.4. Key Overlapping Targets and PPI Network Analysis
GO and KEGG Analysis of Key Overlapping Targets
3.5. Molecular Docking
3.6. Molecular Dynamics Modeling
3.7. MM-GBSA Binding Free Energy
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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ID | Molecule Name | Molecular Formula | Molecular Weight (g/mol) | OB (%) | DL |
---|---|---|---|---|---|
MOL000359 | Sitosterol | C29H50O | 414.7 | 36.91 | 0.75 |
MOL004328 | Naringenin | C15H12O5 | 272.25 | 59.29 | 0.21 |
MOL005100 | Hesperetin | C16H14O6 | 302.28 | 47.74 | 0.27 |
MOL005815 | Citromitin | C21H24O8 | 404.4 | 86.90 | 0.51 |
MOL005828 | Nobiletin | C21H22O8 | 402.4 | 61.67 | 0.52 |
System Name | ΔEvdw | ΔEelec | ΔGGB | ΔGSA | ΔGbind |
---|---|---|---|---|---|
KRAS/crystal_ligand | −40.32 | −2.08 | 20.96 | −6.09 | −27.52 |
AKT1/crystal_ligand | −89.74 | 5.09 | 45.37 | −8.69 | −47.98 |
MTOR/crystal_ligand | −92.13 | −66.12 | 84.56 | −12.32 | −86.01 |
AKT1/Hesperetin | −38.57 | −21.05 | 38.45 | −5.25 | −26.42 |
AKT1/Sitosterol | −63.44 | −2.26 | 31.75 | −7.56 | −41.51 |
KRAS/Hesperetin | −31.51 | −25.38 | 37.85 | −4.40 | −23.44 |
KRAS/Naringenin | −12.45 | −6.64 | 13.90 | −1.62 | −6.81 |
MTOR/Hesperetin | −37.53 | −45.93 | 56.51 | −5.27 | −32.21 |
MTOR/Sitosterol | −47.54 | −2.51 | 18.46 | −5.98 | −37.57 |
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Ullah, A.; Sun, Q.; Li, J.; Li, J.; Khatun, P.; Kou, G.; Lyu, Q. Bioactive Compounds in Citrus reticulata Peel Are Potential Candidates for Alleviating Physical Fatigue through a Triad Approach of Network Pharmacology, Molecular Docking, and Molecular Dynamics Modeling. Nutrients 2024, 16, 1934. https://doi.org/10.3390/nu16121934
Ullah A, Sun Q, Li J, Li J, Khatun P, Kou G, Lyu Q. Bioactive Compounds in Citrus reticulata Peel Are Potential Candidates for Alleviating Physical Fatigue through a Triad Approach of Network Pharmacology, Molecular Docking, and Molecular Dynamics Modeling. Nutrients. 2024; 16(12):1934. https://doi.org/10.3390/nu16121934
Chicago/Turabian StyleUllah, Amin, Qiuxi Sun, Jiangtao Li, Jinjie Li, Pipasha Khatun, Guangning Kou, and Quanjun Lyu. 2024. "Bioactive Compounds in Citrus reticulata Peel Are Potential Candidates for Alleviating Physical Fatigue through a Triad Approach of Network Pharmacology, Molecular Docking, and Molecular Dynamics Modeling" Nutrients 16, no. 12: 1934. https://doi.org/10.3390/nu16121934
APA StyleUllah, A., Sun, Q., Li, J., Li, J., Khatun, P., Kou, G., & Lyu, Q. (2024). Bioactive Compounds in Citrus reticulata Peel Are Potential Candidates for Alleviating Physical Fatigue through a Triad Approach of Network Pharmacology, Molecular Docking, and Molecular Dynamics Modeling. Nutrients, 16(12), 1934. https://doi.org/10.3390/nu16121934