Abstract

The binding site of the macrolides laulimalide and peloruside A, which is different from that of the clinically useful drugs paclitaxel/taxol and ixabepilone (tax site), is known to be between two adjacent beta-tubulin units (ext site). Here, we report our study of the binding of these molecules to an alpha 1 beta 1/alpha 2 beta 2-tubulin "tetramer" model. AutoDock 4.2.6//AutoDock Vina dockings predicted that the affinities of laulimalide and peloruside A for the tax site are quite similar to those for the ext site. However, molecular dynamics (MD) simulations indicated that only when these two ligands are located at the ext site, there are contacts that help stabilize the system, favoring the beta 1/beta 2 interactions. The binding affinity of laulimalide for this site is stronger than that of peloruside A, but this is compensated for by additional beta 1/beta 2 contacts that are induced by peloruside A. MD studies also suggested that epothilones at the tax site and either laulimalide or peloruside A at the ext site cause similar stabilizing effects (mainly linking the M-loop of beta 1 and loop H1-B2 of beta 2). In a "hexamer" model (3 units of alpha beta-tubulin), the effects are confirmed. Metadynamics simulations of laulimalide and peloruside A, which are reported for the first time, suggest that peloruside A produces a stronger change in the M-loop, which explains the stabilization of the beta 1/beta 2 interaction.