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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Molecular docking and dynamic simulation analysis of BPTF with alkaloids
Rohan Daniel Mammen1, Jino Blessy1
1Department of Bioinformatics, Sri Ramachandra Faculty of Engineering and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, India.
Bioinformation
|May 11, 2026
Summary
Sanguinarine chloride shows promise as a BPTF inhibitor for treating medulloblastoma, a pediatric brain tumor. This plant-based compound demonstrated low toxicity and high stability in simulations, suggesting its potential for anti-cancer therapy.
Area of Science:
- Oncology
- Molecular Biology
- Pharmacology
Background:
- Medulloblastoma is a malignant pediatric brain tumor.
- The bromodomain PHD finger transcription factor (BPTF) protein is an epigenetic regulator implicated in tumor progression.
Purpose of the Study:
- To evaluate five plant-based alkaloids as potential inhibitors of the BPTF protein.
- To identify promising compounds for anti-medulloblastoma therapy.
Main Methods:
- Molecular docking and 100 ns molecular dynamics simulations were conducted using PyRx and Desmond.
- Five plant-based alkaloids (Sanguinarine chloride, Coptisine, Chelerythrine, Nitidine, and Chelidonine) were tested against BPTF.
Main Results:
- Coptisine exhibited the highest docking affinity (-6.8 kcal/mol), followed by Sanguinarine chloride and Chelerythrine (-6.6 kcal/mol).
- Sanguinarine chloride displayed low toxicity (protox-III) and high stability during simulations (consistent RMSD 1.0-1.5 Å).
Conclusions:
- Sanguinarine chloride is identified as a highly promising BPTF inhibitor.
- Sanguinarine chloride holds potential for developing novel anti-medulloblastoma therapies.
