Theoretical study on binding interactions of laccase-enzyme from Ganoderma weberianum with multiples ligand substrates with environmental impact

Abstract

Laccase catalyzes oxidation of lignin and aromatic compound with similar structure to this one. Their low substrate specifi city results on degradation of similar phenolic compounds. In this context, Molecular Docking was performed with different ligands suggesting potential biodegradation. Binding active-sites prediction of fungal laccase (access number uniprotkb: A0A166P2X0), from Ganoderma weberianum was performed using machine learning algorithm based on Deep Convolutional Neural Networks (DeepSite-CNNs chemoinformatic tool). Herein, ligands like 2,4-dichlorophenol, benzidine, sulfi soxazole, trimethoprim and tetracycline were analyzed and two additional reference controls which were 2,2-azinobis 3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and 2,6-dimetoxyphenol (2,6 DMP) were used in comparison with the other former mentioned ligands based on high laccase affi nity. The fi ve ligands were carried out because their potential biotechnological interest: the antibiotics sulfi soxazole, trimethoprim and tetracycline, and xenobiotics 2,4-dichlorophenol and benzidine. Molecular docking experiments returned Gibbs free energy of binding (FEB or affi nity) for laccase-ligand complexes. The best docking binding-interaction from each laccase-ligand conformation complexes suggest great ability of these ligands to interact with the laccase active-binding site. Herein, FEB values (kcal/mol) were obtained with higher affi nity values for reference controls like 2,6-dimethoxyphenol with-4.8 Kcal/mol and ABTS with-7.1 Kcal/mol. Furthermore, the FEB values were-4.7,-6.5,-6.8,-5.2 and-6.5 Kcal/mol, for 2,4-dichlorophenol, benzidine, sulfi soxazole, tetracycline and trimethoprim respectively with high prevalence of hydrophobic interaction with functional laccase binding residues. Lastly, this study presents for fi rst time at the bioinformatics fi eld a molecular docking approach for the prediction of potential substrate of laccase from Ganoderma weberianum towards biotechnological application.

Molecular Docking of Lac_CB10: Highlighting the Great Potential for Bioremediation of Recalcitrant Chemical Compounds by One Predicted Bacteroidetes CopA-Laccase

“…The antimicrobial trimethoprim showed an affinity of −6.1 kcal/mol and interacted hydrophobically with His124, which belongs to the conserved motif bound to CuII, Lys412, Met521 (CuIV), Leu410, Pro411 and Tyr95, and established hydrogen bonds with Met520 (CuIV) and Met126 (Figure 7D). The interaction of trimethoprim with CuIV (His479) was also described by Cárdenas-Moreno et al [44], who reported a binding energy of −6.5 kcal/mol, very close to our result.…”

The Impact of Tetracycline Pollution on the Aquatic Environment and Removal Strategies

“…The root mean square deviation of the laccase-tetracycline interaction was 1.991. As lower values indicate higher similarity, it may be concluded that laccase can effectively bind to tetracycline [ 103 ].…”

Oxidoreductase enzymes: Characteristics, applications, and challenges as a biocatalyst

“…3,45 For example, such regions were identified in a G. weberianum laccase toward benzidine, antibiotics, model dyes such as Remazol Brilliant Blue R and Intra, and specific synthetic substrates, such as 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic) acid (ABTS) and 2,6-dimethoxyphenol (DMF) by bioinformatic methods. 74 A similar approach was used to predict the interaction among Trametes maxima laccase, ABTS, DMF, or the dyes acid blue 62, 113, and 116. 7 The T. versicolor laccase has broad substrate specificity, thus biotransforming compounds such as phenols, monophenols, and multisubstituted derivatives, including chlorophenols, nitrophenols, and bisphenols.…”

“…For many of these ligands, the active site regions involved in the interactions have also been characterized 3,45 . For example, such regions were identified in a G. weberianum laccase toward benzidine, antibiotics, model dyes such as Remazol Brilliant Blue R and Intra, and specific synthetic substrates, such as 2,2′‐azino‐bis(3‐ethylbenzothiazoline‐6‐sulfonic) acid (ABTS) and 2,6‐dimethoxyphenol (DMF) by bioinformatic methods 74 . A similar approach was used to predict the interaction among Trametes maxima laccase, ABTS, DMF, or the dyes acid blue 62, 113, and 116 7 .…”