Identification of molecular interactions of pesticides with keratinase for their potential to inhibit keratin biodegradation

Abstract

The recalcitrant, fibrous protein keratin is found in the outermost layer of vertebrate skin, feathers, hair, horn, and hooves. Approximately, 10 million tons of keratin wastes are produced annually worldwide, of which around 8.5 million tons are from feather wastes. The biodegradation of keratin has been a challenge due to the lack of understanding of biological parameters that modulate the process. Few soil-borne microbes are capable of producing keratinase enzyme which has the potential to degrade the hard keratin. However, various pesticides are abundantly used for the management of poultry farms and reports suggest the presence of the pesticide residues in feather. Hence, it was hypothesized that pesticides would interact with the substrate-binding or allosteric sites of the keratinase enzyme and interferes with the keratin-degradation process. In the present study, molecular interactions of 20 selected pesticides with the keratinase enzyme were analyzed by performing molecular docking. In blind docking, 14 out of 20 pesticides showed higher inhibitory potential than the known inhibitor phenylmethylsulfonyl flouride, all of which exhibited higher inhibitory potential in site-specific docking. The stability and strength of the protein complexes formed by the top best potential pesticides namely fluralaner, teflubenzuron, cyhalothrin, and cyfluthrin has been further validated by molecular dynamic simulation studies. The present study is the first report for the preliminary investigation of the keratinase-inhibitory potential of pesticides and highlights the plausible role of these pesticides in hindering the biological process of keratin degradation and thereby their contribution in environmental pollution.

Graphical abstract: Illustration depicting the hypothesis, experimental procedure, and the resultant keratinase-inhibitory potential of selected pesticides.

Keywords: Blind docking; Hydrogen bond; Keratinase; Molecular dynamic simulation; Pesticide; Site-specific docking.

Fig. 1

3D (left) and 2D (right) photographs of 4 best docked pesticides (fluralaner, teflubenzuron, fipronil, cyfluthrin) and the control PMSFwith keratinase enzyme in blind docking study

Fig. 1

3D (left) and 2D (right) photographs of 4 best docked pesticides (fluralaner, teflubenzuron, fipronil, cyfluthrin) and the control PMSFwith keratinase enzyme in blind docking study

Fig. 2

3D (left) and 2D (right) photographs of 4 best docked pesticides (fluralaner, cyhalothrin, teflubenzuron, cyfluthrin) and the control PMSF with keratinase in site-specific docking study

Fig. 2

3D (left) and 2D (right) photographs of 4 best docked pesticides (fluralaner, cyhalothrin, teflubenzuron, cyfluthrin) and the control PMSF with keratinase in site-specific docking study

Fig. 3

Graph showing the relationship between molecular weight of the pesticides and their binding effficiencies to keratinase in blind docking study

Fig. 4

Graph showing the relationship between molecular weight of the pesticides and their binding effficiencies to keratinase in site-specific docking study

Fig. 5

The root-mean-square deviation (RMSD) plots of keratinase and the docked complexes with ligands, En- known inhibitor, En-Cyfluthrin, En-Cyhalothrin, En-Fluralaner and En-Teflubenzuron during the simulation of 50 ns

Fig. 6

The root mean square fluctuation (RMSF) plots of keratinase (Apo-Keratinase) and the docked complexes with ligands, En-known inhibitor complex, En-Cyfluthrin, En-Cyhalothrin, En-Fluralaner and En-Teflubenzuron during the simulation of 50 ns

Fig. 7

Radius of gyration (RG) plot for keratinase protein (Apo-keratinase) and the docked complexes with ligands, En-known inhibitor, En-cyfluthrin, En-fluralaner, En-teflubenzuron, and En-cyhalothrin during the simulation of 50 ns

Fig. 8

Solvent-accessible surface area (SASA) plots for chains B and C for keratinase (Apo-Keratinase) and docked complexes with ligands En-known inhibitor, En-Cyfluthrin, En-Cyhalothrin, En-Fluralaner and En-Teflubenzuron for 50 ns simulation

Fig. 9

Number of H-bond formation in keratinase complex with ligands En-known inhibitor, En-Cyfluthrin, En-Cyhalothrin, En-Fluralaner and En-Teflubenzuron for a simulation period of 50 ns