Molecular modeling of N-terminal domains of NMDA-receptor. Study of ligand binding with N-terminal domains

Using the molecular-graphic complex Sybyl6.7.2, computational construction of spatial models for N-terminal domains (of NR1- and NR2B-subunits) of NMDA-receptor was conducted. On the basis of the constructed models and also CoMFA method the conclusion is made about presence of the binding site for the compounds similar to iphenprodyl in two N-terminal domains of NR1- and NR2B-subunits. The obtained data can be used for constructing new ligands.

Binding site of AMPA-receptor allosteric modulator

The computer molecular docking of piperonyl acid piperidide (BDP) and some its analogs already known as ampakins was conducted for estimating their possible binding with AMPA-receptor glutamate domains in cyclothiazide binding area and for further design of new structures maximally complimentary to the receptor. On the base of the conducted docking it can be suggested that the binding site of BDP (amides of benzodioxane-6-carboxylic and piperonyl acids) analogs is located in AMPA-receptor cyclothiazide binding pocket. It is shown that formation of protein-ligand complexes of AMPA-receptor with benzodioxane-6-carboxylic and piperonyl acid derivatives, similarly to cyclothiazide, proceeds with interaction with Ser497, Leu751, which significance is confirmed by site-specific mutagenesis.