Molecular dynamics simulation study of tubulin dimer interaction with cytostatics

Colchicine, podophylotoxin, and indibulin are natural cytostatics that are used in the treatment of neoplasms. However, application of the compounds is restricted due to their high toxicity and low specificity. Computational experiments modeling tubulin interactions with the cytostatics seem a promising approach to design new analogues of the above-mentioned drugs with higher cytostatic activity and lower toxicity. Therefore, the CHARMM software was used to examine the macromolecules using molecular dynamics and mechanics methods. Particularly, a procedure was applied according to which molecules of each studied cytostatics were placed at several various random positions around the predicted binding site on tubulin. As a result, cytostatic binding regions were identified on the tubulin molecule. It was shown that, during the interaction, structural alterations occurred in these regions that may be responsible for tubulin polymerization. Thus, alterations have been revealed for the first time in the structure of tubulin in the regions of cytostatic binding that can substantially affect its function.