An in silico [correction of insilico] approach to bioremediation: laccase as a case study.
Laccase (E.C. 1.10.3.2) is one of the well-studied enzymes used for bioremediation of xenobiotics such as phenols, anilines, etc. Its broad substrate specificity offers a wide opportunity for screening pollutants in order to predict potential targets for degradation. Present study utilizes protein-ligand docking as a tool to achieve the said. For virtual screening, a set of pollutants were selected from five different industries from EPA. X-ray crystal structures of laccase enzymes were taken from the Brookhaven Protein Data Bank (PDB). Two-dimensional structures of pollutants were downloaded from the NCBI Pubchem, which were further converted into three-dimensional structures using CORINA. Protein-ligand docking was carried out using GOLD. Nearly 30 and 17% of the selected datasets showed the best average GOLD fitness score for fungal and bacterial laccase enzyme respectively, suggesting thereby that laccase might be able to oxidize these pollutants. Moreover, in few cases like anthracene, phenanthrene, etc., there is experimental data to support this hypothesis. Similar kind of work would be helpful to find putative pollutants for other biodegradative enzymes.
Suresh
Panneer Selvam
PS
Environmental Biotechnology Division, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.
Kumar
Anil
A
Kumar
Rita
R
Singh
Ved Pal
VP
D001412:Bacillus subtilis / Q000201:enzymology*; D001487:Basidiomycota / Q000201:enzymology*; D052160:Benzothiazoles / Q000737:chemistry; D001673:Biodegradation, Environmental; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D042845:Laccase / Q000378:metabolism*; D008024:Ligands; D012984:Software; D013451:Sulfonic Acids / Q000737:chemistry
D052160:Benzothiazoles; D008024:Ligands; D013451:Sulfonic Acids; C002502:2,2'-azino-di-(3-ethylbenzothiazoline)-6-sulfonic acid; D042845:Laccase