Structural conservation of the gabapentinoid binding site in human and Caenorhabditis elegans α2δ subunits: a docking and molecular dynamics perspective

Abstract

Pain is a global health burden, highlighting the need for effective therapeutic strategies. Gabapentin (GBP) and pregabalin (PGB), used for neuropathic pain, act primarily through 2{delta} auxiliary subunits of voltage-gated calcium channels. Caenorhabditis elegans expresses UNC-36, an ortholog of mammalian 2{delta} proteins involved in calcium-channel function and nocifensive behavior. However, whether UNC-36 preserves the molecular features required for gabapentinoid recognition remains unclear. We compared human 2{delta}-1 and UNC-36 using sequence and structural analyses, molecular docking, 500-ns molecular dynamics simulations, interaction profiling, principal component and free-energy landscape analyses, and MM/GBSA calculations. UNC-36 preserved the overall architecture of the mammalian gabapentinoid-binding region despite substantial sequence divergence, and both ligands remained associated with the modeled pockets. However, residue-level interaction networks differed between species. Human 2{delta}-1 showed greater contributions from aromatic interactions, whereas UNC-36 relied more prominently on cationic and hydrogen-bond donor interactions mediated by Arg501 and Arg503. The human 2{delta}-1-PGB complex maintained the most stable ligand pose, whereas 2{delta}-1-GBP showed greater positional variation. In UNC-36, PGB exhibited greater deviation from its initial binding pose than GBP. The first two principal components accounted for more conformational variance in UNC-36 complexes than in human complexes. MM/GBSA estimates showed that PGB was energetically favored over GBP in human 2{delta}-1, whereas GBP was favored over PGB in UNC-36. These findings show that conservation of the gabapentinoid-binding architecture is accompanied by species-specific differences in interaction chemistry, conformational dynamics, and estimated binding energetics, providing a molecular basis for interpreting C. elegans gabapentinoid responses in a translational context.