Academic Journal
Evaluation of Structure Prediction and Molecular Docking Tools for Therapeutic Peptides in Clinical Use and Trials Targeting Coronary Artery Disease.
| العنوان: | Evaluation of Structure Prediction and Molecular Docking Tools for Therapeutic Peptides in Clinical Use and Trials Targeting Coronary Artery Disease. |
|---|---|
| المؤلفون: | Alotaiq, Nasser1 (AUTHOR) naalotaiq@imamu.edu.sa, Dermawan, Doni2 (AUTHOR) doni.dermawan.stud@pw.edu.pl |
| المصدر: | International Journal of Molecular Sciences. Jan2025, Vol. 26 Issue 2, p462. 24p. |
| مصطلحات موضوعية: | *MOLECULAR structure, *CORONARY artery disease, *MOLECULAR docking, *PEPTIDES, *APELIN |
| مستخلص: | This study evaluates the performance of various structure prediction tools and molecular docking platforms for therapeutic peptides targeting coronary artery disease (CAD). Structure prediction tools, including AlphaFold 3, I-TASSER 5.1, and PEP-FOLD 4, were employed to generate accurate peptide conformations. These methods, ranging from deep-learning-based (AlphaFold) to template-based (I-TASSER 5.1) and fragment-based (PEP-FOLD), were selected for their proven capabilities in predicting reliable structures. Molecular docking was conducted using four platforms (HADDOCK 2.4, HPEPDOCK 2.0, ClusPro 2.0, and HawDock 2.0) to assess binding affinities and interactions. A 100 ns molecular dynamics (MD) simulation was performed to evaluate the stability of the peptide–receptor complexes, along with Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) calculations to determine binding free energies. The results demonstrated that Apelin, a therapeutic peptide, exhibited superior binding affinities and stability across all platforms, making it a promising candidate for CAD therapy. Apelin's interactions with key receptors involved in cardiovascular health were notably stronger and more stable compared to the other peptides tested. These findings underscore the importance of integrating advanced computational tools for peptide design and evaluation, offering valuable insights for future therapeutic applications in CAD. Future work should focus on in vivo validation and combination therapies to fully explore the clinical potential of these therapeutic peptides. [ABSTRACT FROM AUTHOR] |
| قاعدة البيانات: | Academic Search Index |
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