Mutation studies on degradation of 3-phenoxybenzoic acid by Lacticaseibacillus paracasei – human gut microbiome in controlling risk for Parkinson’s disease using molecular simulation dynamics

Parkinson’s disease (PD) is a debilitating neurodegenerative disease affecting millions worldwide, especially the elderly. Pesticides, particularly pyrethroids like Cypermethrin, have been linked to the development of PD. Cypermethrin, when ingested, is broken down into 3-phenoxybenzoic acid (3PBA), which can lead to the dysfunction or death of dopaminergic neurons. Catechol-2,3-dioxygenase is an enzyme that breaks down 3PBA into catechol, that can further be processed and excreted by the human body. This enzyme is produced by the bacteria Lacticaseibacillus paracasei, a naturally present human gut microbe. Mutation studies were done to study the potential of the human gut microbiome in pesticide degradation improve the activity of the wild-type enzymes in degrading pesticides. The mutations were induced in two subunits of Catechol-2,3-dioxygenase using the WGS sequence of the gene coding for the same. Two subunits of the same protein i.e. Catechol-2,3-dioxygenase and NAD(+) reductase, were subjected to mutations using PyMol v3.1.0, and the crystal structures of the wild-type and mutant were docked against the ligand, 3-Phenoxybenzoic acid, using PyRx v0.8, and visualised using BIOVIA Discovery Studio Visualiser v24.1.0.23298, PyMol v3.1.0 and LigPlot + v2.2.9. The effects of mutation were further studied by analyzing the results of the molecular dynamics simulations conducted using the GROMACS software. Simulation trajectories like RMSD, RMSF, Inter and Intramolecular H-bonds, SASA, RG, PCA, FEL and FEP, all indicated better binding of the ligand (3PBA) to the active site.