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.
This computational study reports targeted mutations in Lacticaseibacillus paracasei catechol-2,3-dioxygenase and NAD(+) reductase that, by docking and molecular dynamics, improve in silico binding of 3‑phenoxybenzoic acid (a cypermethrin metabolite) suggesting enhanced enzymatic degradation…
What the AI sees
This computational study reports targeted mutations in Lacticaseibacillus paracasei catechol-2,3-dioxygenase and NAD(+) reductase that, by docking and molecular dynamics, improve in silico binding of 3‑phenoxybenzoic acid (a cypermethrin metabolite) suggesting enhanced enzymatic degradation…
Research significance
By highlighting a gut‑microbe–based route to degrade a pesticide metabolite linked to Parkinson’s risk, the work suggests microbiome engineering or enrichment could reduce environmental contributors to PD, though it remains purely in silico and needs biochemical and in vivo validation.
Source abstract
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.