Development of a Coarse-grained Simulation Approach to Elucidate Multisite Tubulin-ligand Binding

Microtubules (MTs) are highly dynamic polymers that regulate several cellular functions. The repeating unit is the tubulin heterodimer, which is characterized by a variety of potential binding sites. Elucidating how Microtubule Targeting Agents (MTAs) can interact with the tubulin dimer is of strategic pharmacological importance. Investigations with All-Atom Molecular Dynamics are hindered by the size of the system, hence the idea of applying a Coarse-Grained approach. Martini3 is a wellestablished CG-model that allows to simulate large biomolecules while maintaining a resolution suitable to describe chemical fragments. The starting point has been the modelling of a set of notable MTAs, of the tubulin dimer and of a minimal MT-scaffold. Next, a systematic screening of the influence of ligand and protein representation on the interaction pattern has been performed. Finally, state of the art metadynamics has been applied on a particular case of study both at AA & CG resolution, to compare the different computational predictions. Interestingly, CG-MD equilibrium simulations allow to characterize affinity and kinetics of several binding sites. Furthermore, we observed that CG-metadynamics yields comparable results to AA at a fraction of the cost. Overall, we propose CG-MD as an efficient methodology for exploring ligand binding on challenging multisite targets