Isocitrate lyase (ICL) plays a central role in mobilizing seed lipid reserves by converting fatty acids into sugars during early seedling development. In the present study, a three-dimensional model of ICL was constructed to identify potential ligands through virtual screening simulations. In vitro and in vivo assays were conducted to evaluate the effects of the selected ligands, itaconate and tartrate, on the development of various crop and weed species differing in seed lipid content. The effects of itaconate were assessed in 5-day-old seedlings grown in germination boxes (50-1000μM) and in 14-day-old seedlings grown in pots under greenhouse conditions (0.008-16.25g/dm3). Overall, species with higher seed lipid content exhibited greater sensitivity to itaconate inhibition, particularly during early seedling growth. ICL activity extracted from sensitive species was inhibited by itaconate, whereas tartrate had no effect. As a consequence of its primary action in the glyoxylate cycle, itaconate impaired gluconeogenesis in cotyledons of Euphorbia heterophylla seedlings, reducing sugar export to the roots and thereby inhibiting seedling development. However, the concentrations required to achieve weed mortality in greenhouse-grown plants were substantially high, indicating limited herbicidal efficacy of itaconate. Structural modification of itaconate to enhance interaction with ICL catalytic residues or improve cellular uptake may yield more effective herbicidal candidates. The detailed protein-ligand interaction data provided by the ArThaICL docking model developed in this study represents a valuable tool to guide this optimization process.