Designing and selecting of novel and safe hypothetical herbicide candidate by computational approach

Herbicides play an important role in the efficient production of crops. However, the improper application causes herbicide residues in the environment. This has become one of the environmental issues in Thailand, which has affected the biota and ecosystems. To solve this problem, an effective new non-environmental toxic herbicide candidate needs to be discovered urgently. This motivated to design a novel herbicide candidate with the desired properties. In this work, a total of 243 hit molecules were generated using LigBuilder. After binding calculation by Audodock, Lig_5 was selected based on the lowest of free binding energy whereas the remaining ligands were chosen based on the least cluster number. The binding interactions were analyzed via Discovery Studio Visualizer. The interaction patterns of Lig_5 were highly similar to those of glyphosate. It forms multiple hydrogen bonds with conserved residues in the binding site of the enzyme. Moreover, Lig_5 is an herbicide candidate based on herbicide-likeness property scores. In addition, Lig_5 is a non-ecotoxic compound based on computational calculation. The results proposed Lig_5 as a newly potent herbicide candidate which could be as effective as glyphosate for further synthesis and testing for weed control.