Substrate binding and lipid-mediated allostery in the human organic anion transporter 1 at the atomic-scale

The Organic Anion Transporter 1 is a membrane transporter known for its central role in drug elimination by the kidney. hOAT1 is an antiporter, i.e., it translocates substrate in exchange for α-ketoglutarate. The pharmacological attention is drawn by hOAT1-mediated drug-drug interactions which may lead to adverse effects. Nonetheless, the understanding of hOAT1’s structure and function remains limited due to the absence of resolved structure of hOAT1. However, owing to conserved structural and functional patterns shared within Major Facilitator Superfamily (MFS) that OAT1 belongs to, an opportunity appeared for structure modelling by protein structure prediction tools and molecular dynamics simulations. Taking advantage of formerly validated hOAT1 models, the present work investigated substrate and co-substrate binding to hOAT1, paying attention to allostery between key hOAT1 domains. Dynamic pictures were provided by microsecond-scaled molecular dynamic simulations of hOAT1 OF bounded to adefovir and/or α-ketoglutarate embedded into POPC-based membranes. Our computational approach has revealed key residues of two binding pockets for adefovir. α-Ketoglutarate might bind to the intracellular charge-relay system highly conserved motifs within MFS. Allostery between these binding pockets was also investigated highlighting the active role of the surrounding lipid bilayer. Lastly, using the structure of hOAT1 in OF as well as inward-facing conformation obtained from AlphaFold 2 (AF2) structure prediction tool, we proposed a structural rationalization of transport impairments experimentally observed for 2 significant single nucleotide polymorphisms, namely Arg50His and Arg454Gln. Graphical Abstract Graphical abstract The present work (from left): (i) reveals binding modes of adefovir (top) and α-ketoglutarate (bottom) to hOAT1; (ii) maps Single Nucleotide Polymorphisms on outward-facing (top) and inward-facing (bottom) conformation of hOAT1; (iii) asses the allosteric effect of lipidic environment and presence of substrates. Highlights Adefovir has at least two binding pockets on hOAT1 in the outward-facing conformation. The highly conserved B-motif within MFS is strongly involved in substrate binding. α-Ketoglutarate binds to the intracellular domain of hOAT1 and destabilizes its OF conformation. The lipid membrane bilayer plays an active role in the allosteric communication between intracellular and extracellular domains of hOAT1.