Exploring the Origin of Differential Binding Affinities of Human Tubulin Isotypes αβII, αβIII and αβIV for DAMA-Colchicine Using Homology Modelling, Molecular Docking and Molecular Dynamics Simulations

Tubulin isotypes are found to play an important role in regulating microtubule dynamics. The isotype composition is also thought to contribute in the development of drug resistance as tubulin isotypes show differential binding affinities for various anti-cancer agents. Tubulin isotypes alpha beta(III) and alpha beta(IV) show differential binding affinity for colchicine. However, the origin of differential binding affinity is not well understood at the molecular level. Here, we investigate the origin of differential binding affinity of a colchicine analogue N-deacetyl-N-(2-mercaptoacetyl)-colchicine (DAMA-colchicine) for human alpha beta(II), alpha beta(III) and alpha beta(IV) isotypes, employing sequence analysis, homology modeling, molecular docking, molecular dynamics simulation and MM-GBSA binding free energy calculations. The sequence analysis study shows that the residue compositions are different in the colchicine binding pocket of apii and , alpha beta(III) whereas no such difference is present in alpha beta(IV) tubulin isotypes. Further, the molecular docking and molecular dynamics simulations results show that residue differences present at the colchicine binding pocket weaken the bonding interactions and the correct binding of DAMA-colchicine at the interface of apii and alpha beta(III) tubulin isotypes. Post molecular dynamics simulation analysis suggests that these residue variations affect the structure and dynamics of apii and alpha beta(III) tubulin isotypes, which in turn affect the binding of DAMA-colchicine. Further, the binding free-energy calculation shows that alpha beta IV tubulin isotype has the highest binding free-energy and apiii has the lowest binding free-energy for DAMA-colchicine. The order of binding free-energy for DAMA-colchicine is alpha beta(IV) similar or equal to alpha beta(II) alpha beta(III). Thus, our computational approaches provide an insight into the effect of residue variations on differential binding of apii, apiii and apiv tubulin isotypes with DAMA-colchicine and may help to design new analogues with higher binding affinities for tubulin isotypes.