In silico exploration of lignin peroxidase for unraveling the degradation mechanism employing lignin model compounds

Abstract

Lignin peroxidase is a heme-containing biocatalyst, well-known for its diverse applications in the fields from environmental chemistry to biotechnology. LiP-mediated oxidative catalysis is H₂O₂-dependent, and can oxidize phenolic, and non-phenolic substrates by oxidative cleavage of the C–C and C–O bonds of lignin. In contrast to fungi-derived LiP, the binding affinity of bacterial-derived LiP to lignin at the molecular level is poorly known to date. Tremendous wet-lab studies have been unveiled that provide degradation and biotransformation information on kraft lignin, whilst studies on the completely transformed compounds and the degradation of each transformed compounds simultaneously during degradation are scarce. To gain an understanding of the degradation process using docking, and MDS based studies, we assessed the binding affinity of selected lignin model compounds with bacterial origin LiP and validated such docked complexes exploiting 30 ns molecular dynamics simulations. We selected and picked a total of 12 lignin model compounds for molecular modeling analysis, namely two chlorinated lignin model compounds (monomer) (2-chlorosyringaldehyde and 5-chlorovanillin), eight standard lignin model compounds (veratryl alcohol, syringyl alcohol, sinapyl alcohol, methyl hydroquinone, guaiacol, coniferyl alcohol, catechol, and 4-methoxy phenol), while, two 4-O-5, and β-O-4 linkage-based multimeric model compounds (dimer: 2-methoxy-6-(2-methoxy-4-methylphenoxy)-4-methylphenol; trimer: syringyl β-O-4 syringyl β-O-4 sinapyl alcohol). Far more specific binding residues were observed from XP-Glide docking, as TYR, HIP (protonated histidine), PHE, VAL, ASP, THR, LYS and GLN. The binding affinity was confirmed by the Gibbs free energy or binding energy (ΔG) score; furthermore, it is found that the maximum binding energy seems to be observed for 4-methoxyphenol with a Glide score of −3.438 with Pi–Pi stacking and H-bond type bonding interactions, whilst the lowest XP Gscore as −8.136 with Pi–Pi stacking and H-bond (side chain) type bonding interactions were found for the trimer model compound. The docked complexes were further evaluated for deep rigorous structural and functional fluctuation analyses through high-performance molecular dynamics simulations-DESMOND, after a post simulation run of 30 ns. The RMSD trajectory analyses of the protein-ligands were found to be in the equilibrium state at the end of simulation run for multimeric lignin model compounds. In addition, ionic ligand–protein interaction occurs among chlorinated compounds, while hydrophobic and H-bond contacts have frequently been observed in all lignin-model compounds. The findings herein demonstrate that bacterial LiP can effectively catalyze multiple lignin model compounds, and it might further be used as an effective tool for sustainable mitigation of diverse environmental contaminants.