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Alphafold Modeling and Molecular Docking of Pseudomonas fluorescens Cutinase with Agrochemicals
Summary
AlphaFold modeling and molecular docking showed that Pseudomonas fluorescens cutinase binds strongly to pyrethroid insecticides (cypermethrin at −9.8 kcal/mol, deltamethrin at −9.5 kcal/mol), suggesting this enzyme may degrade agrochemical contaminants. This is relevant to microplastic pollution research as cutinases can also hydrolyze plastic polymers, making this enzyme a candidate for combined agrochemical and plastic bioremediation.
Abstract Cutinases (E.C. 3.1.1.74) are versatile enzymes produced by bacteria and fungi, known for their ability to hydrolyze cutin, a protective plant polyester. These enzymes have gained attention for their potential in agricultural biotechnology, particularly in bioremediation and sustainable pest management. Building upon our previous in silico characterization of Pseudomonas fluorescens cutinase using homology modeling (Phyre 2 ), this study employed AlphaFold, an AI-driven structure prediction tool, to generate a more accurate 3D model of the enzyme. The refined structure was validated using PROCHECK tool, with 93.8% of residues in favored Ramachandran regions, confirming its reliability for molecular docking studies. To assess the enzyme’s potential interactions with agrochemicals, CB-DOCK2 was used to dock the cutinase against eight ligands, including widely used insecticides (chlorpyrifos, malathion, diazinon, cypermethrin, deltamethrin) and herbicides (2,4-D butyl ester, glyphosate, propanil). Comparative analysis revealed strong binding affinities for cypermethrin (−9.8 kcal/mol) and deltamethrin (−9.5 kcal/mol), while moderate interactions were observed with chlorpyrifos (−6.4 kcal/mol), diazinon (−6.5 kcal/mol), and the herbicide propanil (−7.2 kcal/mol). The natural substrate, Cutin-1, exhibited a binding score of −8.0 kcal/mol, providing a reference for evaluating pesticide interactions. These findings suggest that P. fluorescens cutinase may play a role in the binding or degradation of certain synthetic pesticides, particularly pyrethroids and organophosphates. Future studies should include molecular dynamics simulations to assess binding stability and enzymatic assays to validate hydrolysis activity. Additionally, exploring cutinase engineering for enhanced pesticide degradation could open new avenues for eco-friendly bioremediation strategies. This work advances our understanding of bacterial cutinases and highlights their potential applications in sustainable agriculture.