Molecular basis of inhibition of the amino acid transporter B0AT1 (SLC6A19)

The epithelial neutral amino acid transporter B0AT1 (SLC6A19) is the major transporter for the absorption of neutral amino acids in the intestine and their reabsorption in the kidney. Mouse models have demonstrated that lack of B0AT1 can normalize elevated plasma amino acids in rare disorders of amino acid metabolism such as phenylketonuria and urea-cycle disorders. This discovery has resulted in a quest to identify high-affinity selective inhibitors of B0AT1 for the treatment of disorders of amino acid metabolism. Here we employed a medicinal chemistry approach to improve lead compounds that were identified in a previous high-throughput screen. This effort yielded a group of compounds that inhibited B0AT1 with IC50-values of 31-90 nM. High-resolution cryo-EM structures of B0AT1 in the presence of two compounds from this series identified an allosteric binding site in the vestibule of the transporter. Mechanistically, binding of these inhibitors prevents a substantial movement of TM1 and TM6 that is required for the transporter to make a conformational change from an outward open state to the occluded state.