Biological activity and interaction mechanism of the diketopiperazine derivatives as tubulin polymerization inhibitors

Microtubules are a favorable target for development of anticancer agents. In this study, the anti-proliferative activities of plinabulin and six diketopiperazine derivatives were evaluated against human lung cancer cell line NCI-H460 and human pancreatic cancer cell line BxPC-3. The inhibition activities on these microtubules were assessed by tubulin polymerization and immunofluorescence assays. To gain insight into the interaction mechanism of the derivatives and tubulin, a molecular dynamics simulation was performed. We discovered that the diketopiperazine derivatives could prevent tubulin assembly through conformational changes. Molecular Mechanics/Poisson–Boltzmann Surface Area (MM-PBSA) calculations showed that the trend of the binding free energies of these inhibitors was in agreement with the trend of their biological activities. Introducing hydrophobic groups into the A-ring was favorable for binding. Energy decomposition indicated that van der Waals interaction played an essential role in the binding affinity of tubulin polymerization inhibitors. In addition, the key residues responsible for inhibitor binding were identified. In summary, this study provided valuable information for development of novel tubulin polymerization inhibitors as anticancer agents.