In-silico Characterization of Some Natural Molecules as Bioherbicides for the Control of the Parasitic Plant Cuscuta Species

Parasitic plants can cause major losses in agricultural production as an important source of biotic stress. Cuscuta is among the parasitic plant species that are widespread on all continents. The main methods used in the control of these parasitic plants are cultural measures and physical, mechanical, biological, and chemical control. This study aims to characterize plant-active molecules that have deactivation potential against the β-galactosidase enzyme, which plays a role in the attachment of Cuscuta species to the host plant and act as bioherbicides.

In this context, non-mutagenic natural plant herbicides were selected from Dr. Duke's Phytochemical and Ethnobotanical database, and then conformer screening analyses were performed using the molecular mechanics/MMFF method using Spartan software. The method was continued by performing geometry optimizations. Semi-empirical PM6 method was applied for geometry optimizations. QSAR model was created to understand the relationships between the binding energies and physicochemical properties of the studied molecules. Geometry optimizations and scoring studies of binding energies were performed in Spartan'14 and Autodock Vina 1.1.2 software, respectively.

In the study, five commercial chemical herbicides used against Cuscuta spp. were selected as reference molecules and included in the studied molecule set. Later, the methods applied for candidate herbal herbicide molecules were also repeated for commercial chemical herbicide molecules and the obtained results were included in QSAR modeling. In the modeling studies, linear regression analysis was performed between the calculated physicochemical parameters of the molecule set and the binding energies. BIOVIA Discovery Studio software was used to display the results of the macromolecule-ligand docking studies.

According to the results obtained, among 86 plant-derived natural herbicide molecules against Cuscuta spp., Narciclasine, Deoxypodophyllotoxin, and 3-Hydroxyuridine molecules are recommended for further evaluation as natural herbicides, with confirmatory experimental steps suggested.