Exploring the mechanism of action of podophyllotoxin derivatives through molecular docking, molecular dynamics simulation and MM/PBSA studies

Abstract

The chemical structure of a compound directly affects its biological activity, as different functional groups can change a compound’s activity. With this in mind, the current study aims to predict the likely mechanism of action of several podophyllotoxin derivatives whose biological activities have already been documented. The interactions of the derivatives of podophyllotoxin with tubulin (PDB ID: 6NNG) and topoisomerase II (PDB ID: 3QX3), the two recognised targets of podophyllotoxin, were examined using molecular docking experiments. According to the molecular docking result, tubulin, and the investigated variants of podophyllotoxin interact more effectively than topoisomerase. The greatest docking score of the compounds was −12.200 against tubulin and −4.511 against topoisomerase, indicating that tubulin is the target of these drugs. Further to ascertain the strength of the interaction between the best-docked derivatives and the target protein, additional molecular dynamics investigations were also incorporated. With tubulin, the derivatives engage steadily, while with topoisomerase, the ligands shift from the protein’s initial binding site to its DNA binding site. MMPBSA analysis was used to examine the stability of their relationship.

Communicated by Ramaswamy H. Sarma

Keywords:

• Podophyllotoxin
• cancer
• tubulin
• topoisomerase II
• molecular dynamics
• virtual screening

Acknowledgments

The research work was carried out in the laboratory of the Chemistry, Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Prayagraj-India. The Molecular Dynamic simulation results reported in this work were performed on the Central Computing Facility of IIITA, Prayagraj.

Disclosure statement

The authors declare no conflict of interest.

Funding

The author(s) reported there is no funding associated with the work featured in this article.