Identification of 4-Hydroxybenzaldehyde Schiff Base Derivatives as Novel Fungal Chitin Deacetylase Inhibitors via Pocket-Based Design and Molecular Hybridization

Fungal chitin deacetylase (CDA) is a key virulence factor in plant pathogenic fungi, and developing CDA inhibitors represents a promising disease-control strategy. This study optimized the reported <i>Pst</i>CDA inhibitor <b>VS-24</b> by a dual-track strategy integrating pocket-based design and molecular hybridization. The optimized <b>M-09</b> (<i>K</i>_i = 27.5 μmol/L) exhibited 4-5-fold higher activity against <i>Pst</i>CDA than <b>VS-24</b> (<i>K</i>_i = 124 μmol/L). Structure-activity relationship (SAR) and mechanism studies revealed the critical role of the 4-hydroxyl-phenyl group across compounds in enzymatic inhibition through interactions with Zn²⁺ and His207. Additionally, the rhodanine ring in <b>M-09</b> can establish dual hydrogen bonds with Trp174 and Tyr152, enhancing the binding affinity. Moreover, <b>M-09</b> can inhibit infection by <i>Rhizoctonia solani</i>, <i>Pyricularia oryzae</i>, and <i>Botrytis cinerea</i> and exhibited moderate control efficacy against rice sheath blight at 100 μg/mL. With favorable fungicide-likeness, <b>M-09</b> showed strong potential as a candidate for further development of novel antifungal agents targeting CDA.