Computational investigation of BMAA and its carbamate adducts as potential glutamate inhibitors

Computational investigation of BMAA and its carbamate adducts as potential glutamate inhibitors
Isidora Diakogiannaki, Michail Papadourakis, Vasileia Spyridaki, Zoe Cournia, Andreas Koutselos
Journal of Chemical Information and Modeling, 2023

Beta-N-methylamino-L-alanine (BMAA) is a neurotoxic non-protein amino acid, which may reach the human body through the food chain. When BMAA interacts with bicarbonate in the human body, carbamate adducts are produced, which share high structural similarity with the neurotransmitter glutamate. It is believed that BMAA and its carbamate adducts bind in the glutamate binding site of glutamate receptor 2 type AMPA iGluR (GluR2) causing the neurodegenerative effects of diseases such as Alzheimer’s and Parkinson’s diseases. However, the mechanism of BMAA action and its carbamate adducts bound to GluR2 has not been yet elucidated. Here, we investigate the binding modes and the affinity of BMAA, and its carbamate adducts to GluR2 in comparison to the natural agonist, glutamate, in order to understand whether these can act as glutamate inhibitors. Initially, we perform Molecular Dynamics (MD) simulations of BMAA, and its carbamate adducts bound to GluR2 in order to examine the stability of the ligands in the S1/S2 ligand-binding domain of the receptor. In addition, we perform alchemical free energy calculations to compute the difference in the free energy of binding of the beta-carbamate adduct of BMAA to the protein compared to glutamate. Our findings indicate that the carbamate adducts of BMAA have enhanced stability in the binding site of the GluR2 compared to the natural agonist, glutamate. Finally, alchemical free energy results reveal that glutamate and the beta-carbamate adduct of BMAA have comparable binding affinity in the GluR2.

The "Computational investigation of BMAA and its carbamate adducts as potential glutamate inhibitors" container holds the input files and the results of the MD simulations obtained from the NAMD2.14/OPLS-AA and the AMBER20/ff19SB protocols. It also contains the input files and results of the RBFE calculations obtained from NAMD2.14/OPLS-AA/FEP and AMBER20/ff14SB/TI protocols

Note: Provided trajectories have been saved for every 100 ps.

For each system, the following files and directories/folders have been generated:

README.txt

BMAA_inputs/

Amber_MD/
Contains the topology, the force-field parameters and the configuration files to perform 100 ns MD simulations using the AMBER20 software for the alpha-carbamate, beta-carbamate, BMAA and glutamate ligands in complex with the chain A of the GluR2 ligand binding domain.

Amber_TI/
Contains the topology, the force-field parameters and the configuration files to perform FEP/MD simulations using the NAMD 2.14 software for the glutamate->intermediate1, glutamate->intermediate2, intermediate1->beta-carbamate and the intermediate2->beta-carbamate perturbations for the complex and the solvent phases.

NAMD_FEP/
Contains the topology, the force-field parameters and the configuration files to perform FEP/MD simulations using the NAMD 2.14 software for the glutamate->intermediate1, glutamate->intermediate2, intermediate1->beta-carbamate and the intermediate2->beta-carbamate perturbations for the complex and the solvent phases.

NAMD_MD/
Contains the topology, the force-field parameters and the configuration files to perform 100 ns MD simulations using the NAMD 2.14 software for the alpha-carbamate, beta-carbamate, BMAA and glutamate ligands in complex with the chain A of the GluR2 ligand binding domain.

BMAA_outputs/

Amber_MD/
Contains the trajectories (.dcd files) and the .prmtop file from the 100 ns MD simulations using the AMBER20 software and the ff19SB/GAFF2/TIP3P force-field.

Amber_TI/
Contains the energy files (.mdout files) and the .prmtop file from the TI/HREMD simulations using the AMBER20 software, the ProFESSA workflow and the ff14SB/GAFF2/TIP3P force-field.

NAMD_FEP/
Contains the trajectories (.dcd files), the .psf and the .fepout files from the FEP/MD simulations using the NAMD2.14 software and the OPLS-AA force-field.

NAMD_MD/
Contains the trajectories (.dcd files), the .psf and the .pdb files from the 100 ns MD simulations using the NAMD2.14 software and the OPLS-AA force-field.