Computer simulation of xanthotoxin interaction with caspase 3
https://doi.org/10.20538/1682-0363-2026-2-115-120
Abstract
Aim. To perform computer modeling and evaluate the interactions between caspase 3 and xanthotoxin.
Materials and methods. The structures of caspase 3 and xanthotoxin were extracted from the PDB protein database (ID 2J31) and the PubChem chemical compounds and mixtures database (ID 4114), respectively. PyMOL v. 2.5 was used to prepare the caspase 3 structure for docking, and OpenBabel was used to convert xanthotoxin to .pdb format. Molecular docking was performed in AutoDock Vina. Molecular dynamics was performed using GROMACS 2023.3. The CHARMM 36 force field was used to generate the protein topology, and the CHARMM General Force Field (CGenFF) server was used for the ligand topology. Xmgrace and PyMOL were used to analyze the results.
Results. Molecular docking of caspase 3 and xanthotoxin resulted in a stable complex with binding energy of -4.83 kcal/mol. The amino acid residues of caspase 3 involved in intermolecular interaction were identified: tyrosine 195 (TYR195), valine 266 (VAL266), lysine 137 (LYS137). The results of the molecular dynamics simulation confirmed the stability of the complex obtained as a result of docking.
Conclusion. The data obtained indicate the possible role of the studied furocoumarin in the implementation of programmed cell death and can be used for further experimental studies.
About the Authors
N. Yu. Chasovskikh
Siberian State Medical University
Russian Federation
Russian Federation
2 Moskovsky trakt, 634050 Tomsk, Russian Federation
E. E. Shestakova
Siberian State Medical University
Russian Federation
Russian Federation
2 Moskovsky trakt, 634050 Tomsk, Russian Federation
D. E. Novitsky
Siberian State Medical University
Russian Federation
Russian Federation
2 Moskovsky trakt, 634050 Tomsk, Russian Federation
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Review
For citations:
Chasovskikh N.Yu., Shestakova E.E., Novitsky D.E. Computer simulation of xanthotoxin interaction with caspase 3. Bulletin of Siberian Medicine. 2026;25(2):115-120. https://doi.org/10.20538/1682-0363-2026-2-115-120
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