Structural basis of drug recognition by human MATE1 transporter

Ksenija Romane, Giulia Peteani, Somnath Mukherjee, Julia Kowal, Lorenzo Rossi, Jingkai Hou, Anthony A. Kossiakoff, Thomas Lemmin and Kaspar P. Locher ()
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Ksenija Romane: ETH Zürich
Giulia Peteani: Universität Bern
Somnath Mukherjee: The University of Chicago
Julia Kowal: ETH Zürich
Lorenzo Rossi: ETH Zürich
Jingkai Hou: The University of Chicago
Anthony A. Kossiakoff: The University of Chicago
Thomas Lemmin: Universität Bern
Kaspar P. Locher: ETH Zürich

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract Human MATE1 (multidrug and toxin extrusion protein 1) is highly expressed in the kidney and liver, where it mediates the final step in the excretion of a broad range of cationic drugs, including the antidiabetic drug metformin, into the urine and bile. This transport process is essential for drug clearance and also affects therapeutic efficacy. To understand the molecular basis of drug recognition by hMATE1, we determined cryo-electron microscopy structures of the transporter in complex with the substrates 1-methyl-4-phenylpyridinium (MPP) and metformin and with the inhibitor cimetidine. The structures reveal a shared binding site located in a negatively charged pocket in the C-lobe of the protein. We functionally validated key interactions using radioactivity-based cellular uptake assays using hMATE1 mutants. Molecular dynamics simulations provide insights into the different binding modes and dynamic behaviour of the ligands within the pocket. Collectively, these findings define the structural basis of hMATE1 substrate specificity and shed light on its role in drug transport and drug-drug interactions.

Date: 2025
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DOI: 10.1038/s41467-025-64490-z

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