Rational discovery of chitin deacetylase inhibitors against Botrytis cinerea via integrated computational approaches

Gray mold, caused by Botrytis cinerea, leading to great economic loss in agricultural production worldwide. Chemical fungicides represent one of the most effective strategies for preventing and controlling B. cinerea, while confronting increasingly severe resistance and environmental concerns. It is urgent to discover novel environment-friendly fungicides. Chitin deacetylase (CDA), an enzyme involved in chitin deacetylation, represents a promising novel target due to its role in helping pathogens evade plant immunity.

In this work, we employed the AlphaFold3 server to predict the three-dimensional structure of B. cinerea chitin deacetylase (BcCDA). Structure based virtual screening identified the top eight compounds that bind to Zn²⁺ binding pocket of BcCDA. Then, molecular dynamics (MD) simulations and binding free energy calculations confirmed the stable interaction of candidate compounds with BcCDA and identified the residues crucial for the binding. Some of the candidates exhibited ecological safety and low environmental risk. Bioassays demonstrated that 105 244 924 and F0915-6107 showed inhibitory activity against BcCDA and effective prevention of B. cinerea invasion. Surface plasmon resonance (SPR) analysis confirmed the binding of 105 244 924 and F0915-6107 to residues Asp203 and His366 in the Zn²⁺ binding pocket of BcCDA, with K_D values of 2.37 × 10^-6 and 2.84 × 10^-6 mol L^-1, respectively.

These findings indicate that compounds 105 244 924 and F0915-6107 are promising candidates for developing antifungal agents against B. cinerea. © 2026 Society of Chemical Industry.