Structure-based rational design of chemical ligands for AMPA-subtype glutamate receptors.

Ionotropic glutamate receptors (GluRs) function as an excitatory transmitter system in human brain, particularly in learning and memory. Development of small-molecule chemical ligands that selectively potentiate the ion channel activity of AMPA-subtype GluRs would hold promise for treating an exceptionally wide range of disorders including neurodegenerative diseases such as Alzheimer's. Toward this goal, we have obtained nearly complete main-chain NMR resonance assignments of the extracellular ligand-binding domain of GluR2, which enables us to investigate receptor-ligand interactions in physiological conditions at atomic detail. With our NMR structure-based methods, we have discovered several chemical compounds that bind specifically to the GluR2 protein. Notably, our initial lead compounds interact with GluR2 at sites near the interface of receptor dimerization, which plays a pivotal role in controlling receptor gating and desensitization. Our NMR structural analysis further reveals that the regions of GluR2 at the dimer interface exhibit distinct conformational dynamics as compared to the rest of the protein, which we hypothesize to be linked to the mechanisms by which the protein interacts with its ligand, either an agonist or antagonist. This newly discovered relationship of possibly coupling of ligand binding to receptor dimerization, gating and desensitization, which is being further validated, could serve as an excellent in vitro biophysical parameter to evaluate the potential biological effects of the chemical ligands being developed and optimized in our study.