Integrated Analysis, Machine Learning, Molecular Docking and Dynamics of CDK1 Inhibitors in Epithelial Ovarian Cancer: A Multifaceted Approach Towards Targeted Therapy
Abstract
1. Introduction
2. Results
2.1. Microarray Data Analysis
2.2. Differential Expression Analysis of CDK1
2.3. Protein–Protein Interaction Network Analysis
2.4. Proteomic and Survival Analyses
2.5. Molecular Docking Simulation
2.6. Molecular Dynamics Analysis
2.7. Pharmacokinetic Property Analysis
3. Discussion
4. Materials and Methods
4.1. Extraction and Processing of Microarray Data
4.2. Creation of Protein–Protein Interaction Network
4.3. Validation of CDK1 Gene
4.4. Machine Learning in CDK1 Gene Expression
4.5. Pharmacological Effects In Silico
4.6. Statistical Analysis
5. Conclusions
6. Limitations and Future Directions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Prediction | CDK1 (4y72) | WEE1 (8bju) | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Drug | Binding Affinity (kcal/mol) | Binding Site | Hydrophobic Interactions | Hydrogen Bonds | Salt Bridges | Binding Affinity (kcal/mol) | Binding Site | Hydrophobic Interactions | Hydrogen Bonds | Salt Bridges | |
Adavosertib | * | * | * | * | * | −11 | ASN376/CYS379 | 8 | 4 | 1 | |
Alsterpaullone | −10.9 | TYR 15/ASP 86 | 8 | 0 | 0 | −10.4 | CYS379 | 8 | 2 | 0 | |
Avotaciclib | −9.3 | TYR 15/GLN 132 | 5 | 3 | 1 | −8.7 | ASN376/CYS379 | 4 | 5 | 0 | |
Fostamatinib | −12.5 | TYR 15 | 7 | 6 | 0 | −7.5 | ASN376 | 1 | 4 | 2 | |
Olomoucine | −8.5 | TYR 15/GLN 132 | 6 | 4 | 1 | * | * | * | * | * | |
Seliciclib | −8.7 | TYR 15/GLN 132 | 10 | 4 | 0 | * | * | * | * | * | |
Naringin | −10.6 | TYR 15/GLN 132 | 6 | 8 | 0 | −9.6 | ASN376/CYS379 | 5 | 5 | 1 |
Name of the Drug | Admet SAR | |||||||
---|---|---|---|---|---|---|---|---|
Subcellular Localization | AlogP | Molecular Weight | Blood–Brain Barrier | Human Oral Bioavailability | Nephrotoxicity | Hepatotoxicity | Ames Mutagenesis | |
Adavosertib | Mitochondria | 2.89 | 500.607 | + | 0.6429(+) | 0.7773(−) | 0.7075(+) | 0.54(−) |
Alsterpaullone | Mitochondria | 3.24 | 293.276 | + | 0.7143(+) | 0.5739(+) | 0.7875(+) | 0.88(+) |
Avotaciclib | Mitochondria | 0.87 | 281.279 | + | 0.5571(+) | 0.4864(+) | 0.6125(+) | 0.5(−) |
Fostamatinib | Mitochondria | 3.09 | 580.459 | − | 0.5571(+) | 0.7326(+) | 0.6677(+) | 0.53(−) |
Olomoucine | Nucleus | 1.36 | 298.343 | + | 0.5714(−) | 0.5939(−) | 0.5587(+) | 0.58(+) |
Seliciclib | Lysosomes | 3.2 | 354.449 | + | 0.5143(+) | 0.7729(−) | 0.5538(−) | 0.59(−) |
Naringin | Mitochondria | −1.17 | 580.54 | − | 0.9857(−) | 0.6977(−) | 0.8750(−) | 0.61(−) |
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Masoudi, M.; Samadiafshar, S.; Azizi, H.; Skutella, T. Integrated Analysis, Machine Learning, Molecular Docking and Dynamics of CDK1 Inhibitors in Epithelial Ovarian Cancer: A Multifaceted Approach Towards Targeted Therapy. Int. J. Mol. Sci. 2025, 26, 9168. https://doi.org/10.3390/ijms26189168
Masoudi M, Samadiafshar S, Azizi H, Skutella T. Integrated Analysis, Machine Learning, Molecular Docking and Dynamics of CDK1 Inhibitors in Epithelial Ovarian Cancer: A Multifaceted Approach Towards Targeted Therapy. International Journal of Molecular Sciences. 2025; 26(18):9168. https://doi.org/10.3390/ijms26189168
Chicago/Turabian StyleMasoudi, Mahla, Saber Samadiafshar, Hossein Azizi, and Thomas Skutella. 2025. "Integrated Analysis, Machine Learning, Molecular Docking and Dynamics of CDK1 Inhibitors in Epithelial Ovarian Cancer: A Multifaceted Approach Towards Targeted Therapy" International Journal of Molecular Sciences 26, no. 18: 9168. https://doi.org/10.3390/ijms26189168
APA StyleMasoudi, M., Samadiafshar, S., Azizi, H., & Skutella, T. (2025). Integrated Analysis, Machine Learning, Molecular Docking and Dynamics of CDK1 Inhibitors in Epithelial Ovarian Cancer: A Multifaceted Approach Towards Targeted Therapy. International Journal of Molecular Sciences, 26(18), 9168. https://doi.org/10.3390/ijms26189168