Computational protocol: Chenopodium ambrosioides L. Reduces Synovial Inflammation and Pain in Experimental Osteoarthritis

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Protocol publication

[…] The interaction between ascaridole, the main monoterpene found in the C. ambrosioides species, and the pain receptor NMDA was analyzed using molecular docking. The ascaridole structure was obtained from the PubChem database—Code 10545. The terpene geometry was optimized in a vacuum at medium level of Density Functional Theory (DFT) to obtain the atomic and molecular electronic properties that are correlated with biological activity, using a B3LYP hybrid functional with base set 6–31++G (d, p) using Gaussian software 09 (Frisch, Wallingford, CT, USA). Vibrational frequencies were calculated from analytic second derivatives to check the minimum on the potential energy surface. The NMDA receptor structure used was obtained from Rattus norvegicus and was available in the Protein Data Bank (code 4NF5).A protein with a crystallographed glutamatergic receptor was used in the molecular docking assays with NMDA receptors. This protein consists of two chains (A and B) that differ in their amino acid compositions. The ligands present therein were removed, and one docking was performed separately in each chain.The AutoDock 4.2 package [] was used for molecular docking calculations. The AutoDock Tools module was used to prepare and analyze computer simulations. Gasteiger loads and polar hydrogen necessary for the potential calculations were added considering the target structure, with the water molecules removed. The Gasteiger loads were also assigned to the ligands, and the non-polar hydrogens were suppressed. The rotatable interactions of each ligand were defined automatically. AutoDock requires pre-calculated three-dimensional maps, arranged in a box composed of a three-dimensional grid map in a defined region of the macromolecule (target site). AutoGrid 4.0 software was used to generate the maps for the ligands. The box was placed in the catalytic region of the receptor, centered on the portion of the amino acids Tyr143 (Chain A) and Arg121 (Chain B), identified as the active site of the NMDA receptor. The dimensions of the box in the X-, Y- and Z-axes were 60 Å x 60 Å x 60 Å, respectively, with a spacing of 0.375 Å [].The Lamarckian genetic algorithm (LGA) [] was chosen to search for the best conformations, with 100 runs for each ligand (genetic algorithm with local search). During the search process, the NMDA receptor structure was kept rigid while the ligands were kept flexible. The initial population was maintained at 150, and the search was performed using random initial conformations. The complex with the best result was identified based on inhibition constants and residues that best interacted with the ligand. Molecular analyses and complex representations were obtained using the UCSF Chimera package, and representations of hydrogen and hydrophobic interactions were generated using LigPlot++ software [–]. […]

Pipeline specifications

Software tools AutoDock, UCSF Chimera
Application Protein interaction analysis
Organisms Rattus norvegicus
Diseases Osteoarthritis
Chemicals Chondroitin Sulfates, N-Methylaspartate, Glutamic Acid