Chasing the full free energy landscape of neuroreceptor/ligand unbinding by metadynamics simulations

Abstract

Predicting the complete free energy landscape associated with protein-ligand unbinding would greatly help designing drugs with highly optimized pharmacokinetics.Here we investigate the unbinding of the iperoxo agonist to its target human neuroreceptor M 2 , embedded in a neuronal membrane. By feeding out-of-equilibrium molecular simulations data in a classification analysis, we identify the few essential reaction coordinates of the process. The full landscape is then reconstructed using an exact enhanced sampling method, well-tempered metadynamics in its funnel variant. The calculations reproduce well the measured affinity, provide a rationale for mutagenesis data and show that the ligand can escape via two different routes. The allosteric modulator LY2119620 turns out to hamper both escapes routes, thus slowing down the unbinding process, as experimentally observed. This computationally affordable protocol is totally general and it can be easily applied to determine the full free energy landscape of membrane receptors/drug interactions.

On the accuracy of molecular simulation-based predictions of koffvalues: a Metadynamics study

“…4). Taken together, these results are consistent with previous WT-MetaD-based free energy calculations which showed excellent agreement between calculated and experimental affinities for this 21,30 and other systems. This is expected and it is indeed confirmed by countless examples, both in protein-ligand 37 and protein-protein 38 interactions.…”

“…We followed the same protocol as in ref. 21 to build and equilibrate the systems and run MD. Briefly, we obtained the structure from the protein data bank (PDB code: 4MQS 45 ), parametrized the ligand using GAFF, 19 and embedded it in a neuronal-like 26 membrane.…”

“…1), a system that is routinely used in neuroimaging and extensively investigated by some of us in a recent work. 21 First, we calculate the k off value of the ligand by using the Amber14SB force field 22 using well-tempered 23 (WT) and FA-MetaD. To minimize errors due to the modeling procedure, we use the same pH and ionic strength as in the experimental conditions.…”

G Protein-Coupled Receptor-Ligand Dissociation Rates and Mechanisms from τRAMD Simulations

“…Computationally, iperoxo dissociation was simulated using metadynamics by Capelli et.al. 30 Two egress routes of iperoxo through the ECV were observed in these simulations with one being predominant. It was suggested that the presence of the PAM would block dissociation by both routes.…”

“…It was suggested in Ref. 30 , that a change in the position of ECL2 might enable opening of an additional egress route on the other side of ECL2. Although we do not observe sizeable rearrangements of the ECL2 position, the additional egress route ECV3, as well as displacement of the ECV2 channel, are indeed observed in RAMD simulations of iperoxo in the presence of PAM, as discussed above (see also Fig.…”