Structure activity relationships (SAR) study to design and synthesize new tubulin inhibitors with enhanced anti-tubulin activity: In silico and in vitro analysis

Abstract

Tubulysin family of natural products is a class of highly cytotoxic tetrapeptides that induce apoptosis by arresting the mitosis of a cell. In this article, we have analysed 49 reported tubulysin derivatives with known IC50 values to develop two and three-dimensional quantitative structure-activity relationships (2D and 3D QSAR) to explore the critical structural framework required for anti-tubulin activity. In the 2D technique, hologram QSAR (HQSAR models were generated by examining different combinations of the field parameters, number of components, and fragment sizes. Reliability of the best HQSAR model was validated by obtaining optimum values for statistical parameters such as cross-validated (q2 = 0.92) and correlation (r2 = 0.93) coefficients. Further, 3D-QSAR models were generated via CoMFA and CoMSIA methods. In CoMFA, using the Gast-Huck charge assigning method, the best correlation values for q2 and r2coefficients were found to be 0.59 and 0.93, respectively. Whereas in CoMSIA, by considering field contribution parameters such as steric, electrostatic, hydrophobic interactions, and hydrogen bond acceptor ability, a fine model was generated with best cross-validated (q2 = 0.58) and correlation (r2 = 0.94) coefficients values. Tubulysin M is one of the most potent anticancer agents known with an excellent IC50 of 0.02 nM to kill cancer cells. In the present study, tubulysin M co-crystallised with tubulin protein (PDB ID: 4ZOL) was used for molecular docking studies to analyze the drug-protein interactions. The results of QSAR and molecular docking studies were compiled and through in silico studies, structure activity relationships (SAR) were established. The in silico SAR results were utilized to design novel third generation tubulysin derivatives, which are easy to synthesize when compared to complex natural tubulysin derivatives. One of the third generation derivatives, Tub_01, was chemically synthesized and found to have an excellent anticancer activity against cervical cancer cell line (HeLa) with IC50 of 9.4 nM and 88.6 nM for different incubation time.