In silico description of OCTN1 recognition mechanism and the role of sodium in substrate binding

The Organic Cation Transporter Novel 1 (OCTN1), or SLC22A4, is a pivotal element in the transport of organic cations and zwitterions, influencing diverse physiological and pathological processes. Despite its importance, the transported substrates of OCTN1 have been a subject of ongoing debate. This study addresses this gap by presenting a chimeric 3D model of OCTN1, integrating the AlphaFold-generated large extracellular loop 1 (EL1) onto a homology model derived from OCT3. Molecular dynamics simulations unveil domain-specific mobility, emphasizing the impact of EL1 and intracellular loop 4 (IL4) on overall stability. Molecular docking simulations identify cytarabine and verapamil as top-scoring ligands, aligning with their known inhibitory effects on OCTN1. Substrate categorization based on MM/GBSA analysis reveals a correlation between molecular weight and binding affinity to the extracellular recognition site. Key recognition residues, such as Tyr211, Glu381, and Arg469, are identified through interaction analysis. Acetylcholine (Ach) exhibits low interaction energy, supporting its one-directional transport hypothesis towards the extracellular side. The study delves into the role of sodium, suggesting Glu381's involvement in sodium binding. Molecular dynamics simulations at varying Na+ concentrations indicate increased sodium occupancy around Glu381, supporting experimental data linking Na+ concentration to molecule transport. In summary, this research provides valuable insights into OCTN1's 3D structure, substrate preferences, and sodium's role. These findings enhance our comprehension of OCTN1 in physiological and pathological processes, with potential implications for drug development and disease management.