Distinct Binding Mechanisms for Allosteric Sodium Ion in Cannabinoid Receptors

Abstract

The therapeutic potential of cannabinoid receptors is not fully explored due to psychoactive side effects and lack of selectivity associated with orthosteric ligands. Allosteric modulators have the potential to become selective therapeutics for cannabinoid receptors. Biochemical experiments have shown the effects of the allosteric Na+ binding on cannabinoid receptor activity. However, the Na+ coordination site and binding pathway are still unknown. Here, we perform molecular dynamic simulations to explore Na+ binding in the cannabinoid receptors, CB1 and CB2. Simulations reveal that Na+ binds to the primary binding site from different extracellular sites for CB1 and CB2. A distinct secondary Na+ coordination site is identified in CB1 that is not present in CB2. Furthermore, simulations also show that intracellular Na+ could bind to the Na+ binding site in CB1. Constructed Markov state models show that the standard free energy of Na+ binding is similar to the previously calculated free energy for other class A GPCRs.

Mechanistic origin of partial agonism of tetrahydrocannabinol for cannabinoid receptors

“…Docking studies reveal stable docked poses for partial agonists in both the binding pockets. In the antagonist-binding pose, we observed that the partial agonists extend downward toward Na + -binding site similar to THC ( 13 ). These partial agonists bind with similar affinity in agonist and antagonist-binding pocket.…”

“…However, THC alkyl chain (side chain) orientation varies between the two binding poses. In antagonist-like pose 1, it extends toward the conserved sodium-binding site ( 13 , 26 , 27 ) similar to the arm 1 of antagonist, whereas, in antagonist-like pose 2, it orients itself in the direction of agonist-binding site similar to the arm 2 of the antagonist ( Fig. 3 , C and D ).…”

“…To capture the entire THC-binding process, adaptive sampling technique is utilized. This approach has been shown to sample the conformational ensemble of a variety of biological systems ( 27 , 53 , 54 , 55 ) including the ligand-binding process ( 13 , 56 , 57 , 58 , 59 ). In this technique, data from one round of simulation are represented by conformational space of protein by using biological relevant features.…”

“…, allosteric modulator, partial agonist) can be explored for designing therapeutics. We recently studied the binding of a negative allosteric modulator (NAM), sodium ion (Na + ), to cannabinoid receptors (CBs) using molecular dynamics simulation ( 13 ). Simulation revealed important differences in binding site and pathway between CB 1 and CB 2 , which can be exploited to design a selective NAM drug.…”

Interacting binding insights and conformational consequences of the differential activity of cannabidiol with two endocannabinoid-activated G-protein-coupled receptors

“…The unbiased MD simulations suggest a sodium-binding site located in the extracellular domain of the CB 1 receptor Additionally to the detailed description of the ligand binding determinants and the receptor's structural consequence, our simulations also identified a sodium-binding site located in the Frontiers in Pharmacology frontiersin.org extracellular side. Previously, the location of a binding-site at the TM domain of the CB 1 receptor has been identified (Dutta et al, 2022b;Katritch et al, 2014). From our unbiased MD simulations and in both CB 1 complexes, we observed the formation of this extracellular sodium-binding site formed by residues located in the extracellular segment of TM5 and TM6, and the extracellular loop 2.…”