Dynamic mechanism for subtype selectivity of endocannabinoids

Endocannabinoids are naturally occurring lipid-like molecules that bind to cannabinoid receptors (CB₁ and CB₂) and regulate many of human bodily functions via the endocannabinoid system. There is a tremendous interest in developing selective drugs that target the CB receptors. However, the biophysical mechanisms responsible for the subtype selectivity for endocannabinoids have not been established. Recent experimental structures of CB receptors show that endocannabinoids potentially bind via membrane using the lipid access channel in the transmembrane region of the receptors. Furthermore, the N-terminus of the receptor could move in and out of the binding pocket thereby modulating both the pocket volume and its residue composition. On the basis of these observations, we propose two hypotheses to explain the selectivity of the endocannabinoid, anandamide for CB₁ receptor. First, the selectivity arises from distinct enthalpic ligand-protein interactions along the ligand binding pathway formed due to the movement of N-terminus and subsequent shifts in the binding pocket composition. Second, selectivity arises from the volumetric differences in the binding pocket allowing for differences in ligand conformational entropy. To quantitatively test these hypotheses, we perform extensive molecular dynamics simulations (∼0.9 milliseconds) along with Markov state modeling and deep learning-based VAMPnets to provide an interpretable characterization of the anandamide binding process to cannabinoid receptors and explain its selectivity for CB₁. Our findings reveal that the distinct N-terminus positions along lipid access channels between TM1 and TM7 lead to different binding mechanisms and interactions between anandamide and the binding pocket residues. To validate the critical stabilizing interactions along the binding pathway, relative free energy calculations of anandamide analogs are used. Moreover, the larger CB₂ pocket volume increases the entropic effects of ligand binding by allowing higher ligand fluctuations but reduced stable interactions. Therefore, the opposing enthalpy and entropy effects between the receptors shape the endocannabinoid selectivity. Overall, the CB₁ selectivity of anandamide is explained by the dominant enthalpy contributions due to ligand-protein interactions in stable binding poses. This study sheds light on potential selectivity mechanisms for endocannabinoids that would aid in the discovery of CB selective drugs.