Diphenyl ether derivatives occupy the expanded binding site of cyclohexanedione compounds at the colchicine site in tubulin by movement of the αT5 loop

Abstract

Microtubule targeting agents represent a very active arena in the development of anticancer agents. In particular, compounds binding at the colchicine site in tubulin are being deeply studied, and the structural information recently available on this binding site allows structure-directed design of new ligands. Structural comparison of our recently reported high resolution X-Ray structure of the cyclohexanedione derivative TUB075 bound to tubulin and the tubulin-DAMA-colchicine complex has revealed a conformational change in the αT5 loop. By a grid-based computational analysis of the tubulin-DAMA-colchicine binding site, we have identified a new favourable binding area in the colchicine-site that was unexplored by our lead TUB075. Thus, based on a structure-guided design, new cyclohexanedione derivatives have been synthesized and tested for tubulin binding and in cellular assays. As a result, we have identified diphenyl ether derivatives with IC50 values around 10–40 nM against three different tumor cell lines and affinity constants for tubulin similar to that of colchicine around 107 M−1. As expected, they halted the cell cycle progression at G2/M phase at concentrations as low as 0.08 μM.