Molecular Modeling Approaches to Study the Binding Mode on Tubulin of Microtubule Destabilizing and Stabilizing Agents

Abstract

Tubulin targeting agents constitute an important class of anticancer drugs. By acting either as microtubule stabilizers or destabilizers, they disrupt microtubule dynamics, thus inducing mitotic arrest and, ultimately, cell death by apoptosis. Three different binding sites, whose exact location on tubulin has been experimentally detected, have been identified so far for antimitotic compound targeting microtubules, namely the taxoid, the colchicine and the vinka alkaloid binding site. A number of ligand- and structure-based molecular modeling studies in this field has been reported over the years, aimed at elucidating the binding modes of both stabilizing and destabilizing agent, as well as the molecular features responsible for their efficacious interaction with tubulin. Such studies are described in this review, focusing on information provided by different modeling approaches on the structural determinants of antitubulin agents and the interactions with the binding pockets on tubulin emerged as fundamental for antitumor activity.To describe molecular modeling approaches applied to date to molecules known to bind microtubules, this paper has been divided into two main parts: microtubule destabilizing (Part 1) and stabilizing (Part 2) agents. The first part includes structure-based and ligand-based approaches to study molecules targeting colchicine (1.1) and vinca alkaloid (1.2) binding sites, respectively. In the second part, the studies performed on microtubule-stabilizing antimitotic agents (MSAA) are described. Starting from the first representative compound of this class, paclitaxel, molecular modeling studies (quantitative structure-activity relationships – QSAR – and structure-based approaches), performed on natural compounds acting with the same mechanism of action and temptative common pharmacophoric hypotheses for all of these compounds, are reported.

1 Molecular Modeling on Microtubule Destabilizing Agents

1.1 Molecular Modeling on Compounds Targeting the Colchicine Binding Site

1.1.1 Colchicine Site Inhibitors

1.1.2 Ligand-Based Approaches to Colchicine Site Inhibitors

1.1.3 Structure-Based Approaches to Colchicine Site Inhibitors

1.2 Molecular Modeling on Compounds Targeting the Vinca Alkaloid Binding Site

2 Molecular Modeling on Microtubule-Stabilizing Agents

2.1 Molecular Modeling on Paclitaxel and Taxanes

2.1.1 The First Electron Crystallography Structure of α,β-Tubulin/Paclitaxel Complex

2.1.2 The Oxetane Issue

2.1.3 The Paclitaxel Binding Mode

2.2 Epothilones

2.3 Common Pharmacophores

2.4 Other Stabilizing Agents

2.4.1 Discodermolide and Dictyostatin

2.4.2 Sarcodictyins and Eleutherobins

2.4.3 Laulimalide and Peloruside

3 Conclusions

References