bioRxiv (2022) 10.1101/2022.05.03.490502
The human L-type amino acid transporter 1 (LAT1; SLC7A5) is a membrane transporter of amino acids, thyroid hormones, and drugs such as the Parkinson’s disease drug L-Dopa. LAT1 is found in the blood-brain-barrier (BBB), testis, bone marrow, and placenta, and its dysregulation has been associated with various neurological diseases such as autism and epilepsy as well as cancer. In this study, we combine metainference molecular dynamics (MD) simulations, molecular docking, and experimental testing, to characterize LAT1-inhibitor interactions. We first conducted a series of molecular docking experiments to identify the most relevant interactions between LAT1’s substrate binding site and ligan ds, including both inhibitors and substrates. We then performed metainference MD simulations using cryo-EM structures in different conformations of LAT1 with the electron density map as a spatial restraint, to explore the inherent heterogeneity in the structures. We analyzed the LAT1 substrate binding site to map important LAT1-ligand interactions as well as newly described druggable pockets. Finally, this analysis guided the discovery of previously unknown LAT1 ligands using virtual screening and cellular uptake experiments. Our results improve our understanding of LAT1-inhibitor recognition, providing a framework for rational design of future lead compounds targeting this key drug target.