Cyanide Hydratase Modification Using Computational Design and Docking Analysis for Improved Binding Affinity in Cyanide Detoxification

Abstract

Cyanide is a hazardous and detrimental chemical that causes the inactivation of the respiration system through the inactivation of cytochrome c oxidase. Because of the limitation in the number of cyanide-degrading enzymes, there is a great demand to design and introduce new enzymes with better functionality. This study developed an integrated method of protein-homology-modelling and ligand-docking protein-design approaches that reconstructs a better active site from cyanide hydratase (CHT) structure. Designing a mutant CHT (mCHT) can improve the CHT performance. A computational design procedure that focuses on mutation for constructing a new model of cyanide hydratase with better activity was used. In fact, this study predicted the three-dimensional (3D) structure of CHT for subsequent analysis. Inducing mutation on CHT of Trichoderma harzianum was performed and molecular docking was used to compare protein interaction with cyanide as a ligand in both CHT and mCHT. By combining multiple designed mutations, a significant improvement in docking for CHT was obtained. The results demonstrate computational capabilities for enhancing and accelerating enzyme activity. The result of sequence alignment and homology modeling show that catalytic triad (Cys-Glu-Lys) was conserved in CHT of Trichoderma harzianum. By inducing mutation in CHT structure, MolDock score enhanced from −18.1752 to −23.8575, thus the nucleophilic attack can occur rapidly by adding Cys in the catalytic cavity and the total charge of protein in pH 6.5 is increased from −6.0004 to −5.0004. Also, molecular dynamic simulation shows a stable protein-ligand complex model. These changes would help in the cyanide degradation process by mCHT.

Cyanide Biodegradation by Trichoderma harzianum and Cyanide Hydratase Network Analysis

“…Cyanide hydratase has been shown to be the key enzyme in the cyanide degradation pathway in previous studies [ 23 ]. This study confirmed the importance of cyanide hydratase in pathway determination using KEGG orthology; K10675 in the Trichoderma genus.…”

Application Potential of Cyanide Hydratase from Exidia glandulosa: Free Cyanide Removal from Simulated Industrial Effluents

“…The activities of the whole E. coli cells (153-600 U/mg dry weight) and CFE (736 U/mg protein) [33] were substantially higher in comparison with the endogenous enzymes, whereas the activities of the purified enzymes from the homologous and heterologous producers were similar (100-1324 U/mg protein; Table S1) [29,31,33]. Further enhancement of CynH action on fCN may be possible by the specific mutations recently proposed in silico [34].…”