Prediction and assessment of energetically-favored binding orientation of cannabidiol at hNav1.1 channel using all-atom molecular dynamics simulations

Epilepsy is a debilitating condition affecting ∼65 million people globally, with ∼3.4 million cases in the United States alone. Cannabidiol (CBD) has shown promise in treating drug-resistant epilepsy, and there are some experimental indications that its effects result from modulation of the human voltage-gated sodium channel 1.1 (hNav1.1), yet the detailed CBD binding to hNav1.1 at molecular level remains poorly understood. Despite prior molecular modeling and mutagenesis studies, no NMR or X-ray structures of CBD-bound hNav1.1 are available, leaving its exact binding orientation undefined. In this study, we investigated the potential binding-site orientation and interactions of CBD within hNav1.1 using computational methods, including docking, Prime-MMGBSA and all-atom molecular dynamics simulations (MD). To gain insight regarding potential binding orientations of CBD within hNav1.1, we performed Induced-Fit Docking of CBD on a cryo-EM structure (PDB ID:7DTD). We evaluated two orientations of CBD within hNav1.1: one in which the cyclohexene moiety is directed towards the central cavity near key residue Phe1772 (Pose A) and another in which the cyclohexene moiety is exposed towards the membrane (Pose B). Subsequent 500 ns MD simulations revealed that Pose B, with the cyclohexene moiety oriented extracellularly towards the membrane within hNav1.1, was energetically more favorable (ΔG = -51.88 ± 5.19 kcal/mol) than the intracellular orientation Pose A (ΔG = -41.57 ± 3.24 kcal/mol). These findings provide valuable insights for designing novel CBD analogs with optimal fit for the hNav1.1 binding pocket.