Riccardo Capelli, Wenping Lyu, Viacheslav Bolnykh, Simone Meloni, Jógvan Magnus Haugaard Olsen, Ursula Rothlisberger, Michele Parrinello, and Paolo Carloni (2020).
The journal of physical chemistry letters, 10.1021/acs.jpclett.0c00999.   (PubMed)

The koff values of ligands unbinding to proteins are key parameters for drug discovery. Their predictions based on molecular simulation may under- or overestimate experiment in a system- and/or technique-dependent way. Here we use an established method-infrequent metadynamics, based on the AMBER force field-to compute the koff of the ligand iperoxo (in clinical use) targeting the muscarinic receptor M2. The ligand charges are calculated by either (i) the Amber standard procedure or (ii) B3LYP-DFT. The calculations using (i) turn out not to provide a reasonable estimation of the transition-state free energy. Those using (ii) differ from experiment by 2 orders of magnitude. On the basis of B3LYP DFT QM/MM simulations, we suggest that the observed discrepancy in (ii) arises, at least in part, from the lack of electronic polarization and/or charge transfer in biomolecular force fields. These issues might be present in other systems, such as DNA-protein complexes.

This work describes an example of using Metadynamics in kinetic calculations.