Fig. 5: Experimental and computational analysis of LGIC binding and selectivity.
From: C5 methylation confers accessibility, stability and selectivity to picrotoxinin
a Relative potencies of PXN and 5MePXN analogs at GABAAR ([3H]-TBOB, n = 1); (b) Relative potencies of PXN and 5MePXN analogs at RDL receptors measured by electrophysiology as a proxy for channel binding (n = 4); (c) Selectivity between vertebrate (GABAA) and invertebrate (RDL) receptors by PXN analogs: C5-methylated analogs are selective for invertebrate receptors; (d) Pairwise identity matrix of GABA/RDL residues across species; (e) PXN (1) and analog 30 in the rat GABA homology model, showing crystal binding poses of PXN (PDB: 6×40; dark gray), PXN after MD (pink), and 30 (light gray) interacting with T287 (β2), T309 (γ2), and T280 (α2). The binding free energy of 30 is predicted to be 1.8 ± 1.5 kcal/mol above that of 1 at GABAA. Orientation of the binding pocket is kept fixed to allow direct comparison of binding poses; (f) PXN (1) and analog 30 in the fly RDL homology model. Crystal binding poses of PXN (PDB: 6 × 40; dark gray), PXN after MD (pink), and 30 (light gray) show varying degrees of interaction with the fly RDL homopentamer. After forcefield minimization, the crystal and MD poses of PXN converged. Interactions with S286, A290, and T294 are indicated with dotted lines.
