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

The Organic Cation Transporter Novel 1 (OCTN1), also known as SLC22A4, is essential for the transport of organic cations and zwitterions, influencing various physiological and pathological processes. Despite its significance, the specific substrates and mechanisms of OCTN1 remain unclear. This study aims to address this gap by constructing a chimeric 3D model of OCTN1, integrating the AlphaFold-predicted large extracellular loop 1 (EL1) with a homology model based on the OCT3 experimental structure. Using molecular dynamics (MD) simulations, we reveal domain-specific mobility, highlighting the stabilizing roles of EL1 and intracellular loop 4 (IL4). Molecular docking and subsequent MD simulations identify cytarabine and verapamil as top-scoring ligands, consistent with their known inhibitory effects on OCTN1. Substrate categorization through MM/GBSA analysis shows a correlation between molecular weight and binding affinity to the extracellular recognition site. Interaction analysis identifies key recognition residues, such as Tyr211, Glu381, and Arg469. Acetylcholine (Ach) exhibits low interaction energy, supporting its hypothesized unidirectional transport towards the extracellular side. Additionally, our study investigates the role of sodium in OCTN1 function, suggesting Glu381's involvement in sodium binding, corroborated by 3D-RISM analysis. MD simulations at varying Na+ concentrations demonstrate increased sodium occupancy around Glu381, aligning with experimental observations linking Na+ levels to transporter activity. In summary, this research provides valuable insights into OCTN1's 3D structure, substrate preferences, and the role of sodium. These findings enhance our comprehension of OCTN1 in physiological and pathological processes, with potential implications for drug development and disease management.