Comparative Binding Energy (COMBINE) Analysis Supports a Proposal for the Binding Mode of Epothilones to β‐Tubulin

The conformational preferences of epothilone A (EPA) and a 12,13‐cyclopropyl C12‐epimerized analogue were explored in aqueous solution using molecular dynamics simulations. The simulated conformers that provided an optimal fit in the paclitaxel binding site of mammalian β‐tubulin were then selected. The resulting modeled complexes were simulated before and after refinement of the M‐loop to improve the fitting and assess ligand stability within the binding pocket. The tubulin‐bound conformation of EPA was found to be unlike a previously reported solution obtained through mixed crystallographic/NMR/modeling studies. However, our conformation was in agreement with an NMR‐based proposal although the exact binding pose within the site was different. Molecular models were built for the complexes of 14 epothilone derivatives with β‐tubulin. A projection to latent structures regression method succeeded in providing a good prediction of the experimentally measured binding enthalpies for the whole set of ligands by assigning weights to a selection of interaction energy terms. These receptor‐based, quantitative structure–activity relationships support the proposed binding mode, help confirm and interpret previously acquired experimental data, shed additional light on the effect of several β‐tubulin mutations on ligand binding, and can potentially direct further experimental studies.