Objective:

We aim to design peptides to specifically inhibit anti-NMDA receptor autoantibodies using molecular modelling in-silico.

Background:

Anti-NMDA receptor (NMDA-R) encephalitis is a severe autoimmune disease caused by autoantibodies against the NR1 subunit of the NMDA-R in the brain, resulting in severe neurologic symptoms. Immunomodulatory/immunosuppressive therapies are first-line treatments but are non-specific and can suppress the overall immune system.

Design/Methods:

Protein interaction analysis was performed between the NMDA-R NR1 subunit and the anti-NMDA-R antibody in the crystal structure from protein data bank 8VUJ. Residue scanning analysis was then performed on the interacting residues to analyze the stability of mutants in the antibody interaction site compared to the wild type. Peptide Nano-Enzymes (PepNzymes) were engineered from the NMDA-R NR1 subunits for the stable mutants using protein linker design to connect smaller peptides. Prime Molecular Mechanics/Generalized Born Surface Area (MM-GBSA) was then used to calculate the binding energy difference of the mutants compared to the wild type.  All calculations were performed using Schrodinger Suite.

Results:

Protein interaction analysis revealed residues 355-380 had interactions at the binding site of the NMDA-R NR1 subunit and anti-NMDA-R antibody.  The residue scanning analysis showed that the mutated residues 360R, 357M, and 358R had exhibited increased binding stability (-17.029, -16.936, and -7.339 kcal/mol, respectively). Using Prime MM-GBSA, we identified 6 PepNzymes with higher binding free energies, with the lead molecular mimic targeting the 357I mutant (free energy of -76.92 kcal/mol, compared to -26.04 kcal/mol for the wild type).  

Conclusions:

In conclusion, we identified 6 PepNzymes resembling the NMDA-R, with binding stability up to three times that of the original. These PepNzymes could be used to develop NMDA-R NR1 molecular mimics, saturating the autoantibodies and potentially treating anti-NMDA autoimmune encephalitis.