Major depressive disorder affects about 6-16% of the world’s population and even leads to suicide. Antidepressants targeting the monoamine system require prolonged treatment over weeks or months and are ineffective in one-third of patients. Ketamine-based antidepressants suggest a promising alternative.

In a study published in Nature, researchers from Dr. ZHU Shujia’s lab at the Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology of the Chinese Academy of Sciences (CAS), together with Dr. LUO Cheng’s team at the Shanghai Institute of Materia Medica of CAS, have revealed the structural basis of antidepressant ketamine action on human N-methyl-D-aspartate (NMDA) receptors. Their research describes the structural basis of ketamine binding and action on human NMDA receptors and paves the way for the future development of ketamine-based antidepressants. 

Ketamine is a pore blocker of the NMDA receptors, which are important glutamate-gated ion channels in the brain. Previous studies have revealed that ketamine can inhibit the channel activity of the NMDA receptors on the synaptic membrane to regulate synaptic plasticity and further rescue stress-induced dendritic spine loss in the cortex and hippocampus. Thus, it is important for the development of ketamine-based antidepressants to illustrate the binding site of ketamine in the NMDA receptors and the structural basis of ketamine’s action on the NMDA receptor. 

In this study, the researchers determined the cryo-EM structure of both human GluN1-GluN2A and GluN1-GluN2B NMDA receptors in the ketamine bound state. They eventually found the electron density map of ketamine in the transmembrane domain of both NMDA receptors. 

The results confirm that the binding pocket of ketamine is in the central vestibule between the channel gate and the selectivity filter. The vestibule is formed by hydrophobic valine (V644 in GluN1 subunits) and leucine (L642 in GluN2A subunits), while the top and bottom of the vestibule are formed by polar threonine and asparagine, respectively. 

To gain more insight into the interaction between ketamine and the residues around the vestibule, the researchers carried out the molecular dynamics simulation to analyze the mobility of ketamine in the binding pocket. 

The results show that L642 in GluN2A made the greatest contribution to relative binding energy during ketamine binding through hydrophobic interaction, while N616 in GluN1 at the bottom formed hydrogen bond with ketamine. These two amino acids, L642 in GluN2A and N616 in GluN1, were identified as key residues forming hydrophobic interactions and hydrogen bonds with ketamine, respectively. In addition, mutations at these two key residues led to ketamine’s reduced potency in blocking NMDA receptor channel activity.