Tom Dixon, Arzu Uyar, Shelagh Ferguson-Miller, and Alex Dickson (2020).
Biophysical journal, 10.1016/j.bpj.2020.11.015.   (PubMed)

The translocator protein (TSPO), previously known as the peripheral benzodiazepine receptor, is of longstanding medical interest as both a biomarker for neuroinjury and a potential drug target for neuroinflammation and other disorders. Recently it was shown that ligand residence time is a key factor determining steroidogenic efficacy of TSPO-binding compounds. This spurs interest in simulations of (un)binding pathways of TSPO ligands, which could reveal the molecular interactions governing ligand residence time. In this study, we use a weighted ensemble algorithm to determine the unbinding pathway for different poses of PK-11195, a TSPO ligand used in neuroimaging. In contrast with previous studies, our results show that PK-11195 does not dissociate directly into the solvent but instead dissociates via the lipid membrane by going between the transmembrane helices. We analyze this path ensemble in detail, constructing descriptors that can facilitate a general understanding of membrane-mediated ligand binding. We construct a set of Markov state models augmented with additional straightforward simulations to determine pose-specific ligand residence times. Together we combine over 40 μs of trajectory data to form a coherent picture of the ligand binding landscape. We find that multiple starting poses yield residence times that roughly agree with the experimental quantity. The ligand binding transition states predicted by these Markov state models occurs when PK-11195 is already in the membrane and involves only minimal ligand-protein interactions. This has implications for the design of new long residence-time TSPO ligands.

This work describes an example of using Weighted Ensemble Molecular Dynamics (WEMD) in kinetic calculations.

The following methods are also used: