Combining Molecular Docking and Molecular Dynamics Simulations to Explore the Binding Affinity and Interactions of Berberine with Wild-Type and Mutated Phosphatase and Tensin Homolog (PTEN)

Abstract

Background: We aimed to find the role and effect of berberine on wild type Phosphatase and Tensin Homolog (PTEN) and mutated type PTEN by utilizing molecular techniques.

Methods: This investigation executed in bioinformatics center of Ghalib University, Kabul, Afghanistan in 2024. To evaluate the binding interactions and affinity of berberine with both wild-type and mutated PTENs, molecular docking was carried out using the Autodock 4.2.2 software. This analysis was followed by molecular dynamics (MD) simulations, which provided insights into the structural dynamics of the complexes. The simulations were performed utilizing the AMBER99SB force field and using the GROMACS 2019.6 software.

Results: Our research on berberine and Wild-type PTEN and mutant PTEN, by utilizing molecular docking and molecular dynamics simulation approaches showed adequate binding affinity and binding energy between both complexes. Docking result parameters shows -7.37 binding energy for wild PTEN, and -6.28 for mutated PTEN. Which means that berberine has more binding affinity with wild PTEN compared with mutated PTEN.

Conclusion: Using advanced computational techniques such as molecular docking and molecular dynamics simulations, this study highlights the potential of Berberine—a natural compound known for its diverse health-promoting properties—as a promising therapeutic candidate for treating cancers linked to PTEN dysfunction.