In Silico Study of Glyphosate Substitute against Rice Weeds as Bioherbicides Candidate

Abstract

Weeds on rice plants have a lot of negative impacts on plant productivity. The majority of approaches in controlling weeds in rice used herbicides including the use of glyphosate as a synthetic herbicide. However, using glyphosate in the long-term results in soil and water pollution accumulation, resulting in decreased soil fertility. This study aims to find new herbicide candidates by mimicking glyphosate's mechanism in inhibiting EPSP synthase, ACCase and photosystem II found in three types of weeds (broad-leaved and grasses and sedges). Representatives of the three types are Monochoria vaginalis (broad-leaved weeds), Cyperus rotundus (sedges) and Eleusine indica (grasses). The PyRx AutoDoc Vina docked fourteen potential bioherbicide candidate compounds at specific sites. The binding affinity value is calculated and ranked to determine the best compound as a bioherbicide candidate. In predicting biological activity, the discovery studio visualized the interaction of each complex. Benzoate and Cinmethylin are the most potent compounds as bioherbicide candidates with binding affinities of -8.2 and -6.9 kcal/mol. This interaction shows 50-59% similarity with glyphosate, so this compound inhibits PEP synthesis, amino acid biosynthesis, photosynthesis and controlling weeds in rice plants.