Kainate Receptor Structural Analysis

Since Occidentalin-1202(s) showed a potent antiepileptic performance in the KA-induced acute epileptic model, one hypothesis is that the peptide may interact with kainate receptors. Kainate-agonist receptors were searched in the Protein Data Bank (https://www.rcsb.org/). After filtering for no mutated structures and kainate affinity, ionotropic glutamatergic receptors GluR5 and GluR6 were chosen. This screening gave eight structures, that were superimposed to carry out the alignment of the sequences. A high similarity among the targets was pointed out, with an identity of 84.3% and similarity of 93.5% (Supplementary Fig. 12).
Regarding the crystallographic structures of the receptor, it was possible to verify a good overlap, and a well-preserved position of the connection site between the structures (Supplementary Fig. 13). The average RMSD between all aligned structures was around 1 Å (Supplementary Table 1). Following, two of the best-resolved PDB structures were used to evaluate the kainate binding site, 2XXR (resolution 1.60 Å) and 2XXT (resolution 1.90 Å). Both represent the same GluR6 receptor, but crystallographic structures were obtained with glutamate and kainate in the binding site, respectively. The two PDB structures were aligned and superimposed (RMSD = 0.693 Å), allowing to evaluate kainate ligand domain, showing that both agonists share the same binding site (Supplementary Fig. 14), although glutamate interacts with more residues than kainate (Supplementary Fig. 15).