Colchicine Binding Site Ligands: A Mechanistic Insight into their Influence and Dual Role

The mechanism of disfavouring the growth of microtubule (MT) by a class of compounds occupying a binding pocket of the constituent protein dimer of α,β-tubulin, is not just about its tightness of association with tubulin; instead it is more about the capacity of the ligand to induce subtle yet global conformational changes and making the dimer incompatible to the MT superstructure. Colchicine binding site is known for harbouring various kinds of such small molecules. Although they compete for the same binding pocket at the junction of the dimer; yet, their phenotypic outcome differs: some of them are more potent than others in arresting the cell cycle to antagonize mitosis, whereas some others appear better as vascular disrupting agents (VDAs), with higher impact on the cytoskeleton of the cells formed by the same dimer. How the small molecules differing in shape, size and chemical structure occupying the same binding pocket of the drug target can all act as destabilizing ligands, yet distinctly diverge in their functions? All-atom molecular dynamics simulation (~5.6 µs) has identified that each ligand has its customized way of influencing the complex network of intra- and inter-molecular interactions. The preference for the two distinct conformational states is linked to the preference for twisting or bending modes of internal motions of the complex. The milder influence of a ligand makes it a VDA (TUB092) and the stronger impact makes the classical ligand Colchicine (COL) an anti-mitotic agent (AMA); whereas the other two ligands BAL27862 (2RR) and Nocodazole (NZO) falls in the intermediate zone. Apart from differentiating the molecular mechanisms of VDA and AMA this work proceeds further to dig into the overall allosteric mechanisms involved with ligand binding at the Colchicine Binding Site (CBS). The detailed investigation on which, led to the detection of important hubs for allostery and the revelation of key contacts, leading to a positive allosteric effect on the tubulin dimer upon each ligand binding.