Computational insights into herbicide resistance via acetohydroxyacid synthase in Ambrosia artemisiifolia

Herbicide resistance poses a major challenge in modern weed management, especially under the pressure of intensive herbicide use and climate-induced stressors. Ambrosia artemisiifolia (common ragweed) is a highly invasive species often controlled by herbicides targeting acetohydroxyacid synthase (AHAS), an enzyme essential for branched-chain amino acid synthesis. Genomic analyses have identified the Trp574Leu mutation as the main driver of resistance to AHAS-inhibiting herbicides. In this study, we employed a suite of in silico techniques, including homology modeling, molecular docking, dynamics simulations, and pharmacophore modeling, to investigate the structural and functional impact of the Trp574Leu mutation in both wild-type and mutant AHAS variants. Key residues in herbicide binding were characterized using molecular dynamics, revealing that the Trp558Leu mutation alters the binding interface by selectively disrupting key wild-type-specific interactions while promoting alternative contacts in the mutant system. Interactions mediated by Ala637, which substantially contribute to the WT binding mode, are markedly reduced in the mutant, whereas contacts involving Arg361 are significantly stabilized. Pharmacophore models were developed for both enzyme variants, with the wild-type model (A1A3A5N12) showing predictive performance (ROC = 0.89, AUAC = 0.88, EF1 % = 7.65) based on cloransulam-methyl binding. A consensus pharmacophore integrating features from both models was constructed to support the rational design of novel herbicides. These results offer molecular-level insights into AHAS-mediated resistance and tools that may aid the rational design of new herbicides capable of overcoming the Trp574Leu resistance mechanism.