Searching of Novel Herbicides for Paddy Field Weed Management—A Case Study with Acetyl-CoA Carboxylase

Abstract

Weed management is the major biological constraint in paddy (Oryza sativa L.) producing areas. Predominantly, barnyard grass (Echinochloa crus-galli) is a rice-mimicking weed that causes 57% of yield loss in rice production. Conventionally, herbicides are the site-specific weed inhibitors often used to suppress E. crus-galli growth. Acetyl-CoA carboxylase (ACCase) is an important target for developing novel herbicides with remarkable selectivity against gramineous weeds. Notably, fenoxaprop-P-ethyl (FPPE) is a selective ACCase herbicide extensively used in paddy fields to inhibit barnyard grass. However, prolonged use of FPPE herbicide elicits phytotoxicity in cultivated rice and herbicide resistance in weeds. Recently, phytotoxins are emerging as an alternative to commercial herbicides with safer environmental profiles. Nevertheless, discovering natural herbicides through in vivo and in vitro techniques is time-consuming and expensive. Therefore, high-end computational screening strategies including Tanimoto similarity, docking, binding free energy, and herbicide-likeness were used to pinpoint the lead molecule. Finally, molecular dynamics and MM/PBSA calculations were employed to validate the binding kinetics of the hit compound. Indeed, sinigrin was identified as a promising phytotoxic inhibitor against the ACCase enzyme. The findings of our study were well correlated with the existing experimental results. Overall, the current work will aid in the development of commercializing phytotoxin herbicides in foreseeable future.