Molecular Interaction Of Acetyl-Coa Carboxylase (Accase) With Fenoxaprop-P Ethyl Through Computational Analysis

Abstract

Herbicides are critical in preventing crop production losses in no-till systems because of their weed-control capabilities as well as their ability to preserve rising soil. Weed resistance to herbicides must be reduced because it is a critical control feature on behalf of diet security. Cross resistance may happen through herbicides from very similar or diverse herbicide families, as well as beside the similar or dissimilar site of action. Weed struggle in the direction of herbicides must be reduced since it is a critical control feature designed for diet protection. The objective of research to determine the enzyme ACCase interaction with the fenoxaprop-p-ethyl as a protein ligand interaction and Molecular dynamics MD simulation analysis to confirm the physical movement of atoms and molecule. Various computational methods and tools were used to find out interaction i.e., RCSB PDB, PubChem, MGL Auto dock vina, Discovery studio, UCSF Chimera, Desmond Schrodinger, and Maestro Schrodinger. The result was concluded that herbicide protein binds to the active site on the receptor at specific location. The 3jzf protein bind with the ARG_292 and make good interaction, the HIS_209 make Hydrophobic bond, GLN_233 and GLN_237 make good hydrogen bond and HIS_236 make water bridges. These residues make excellent interaction with the surrounding residues in 3jzf protein with the ligand Fenoxaprop-p ethyl, ASP_382 is the most important ones in terms of H-bonds for (3jzi) that is not stable bonding. The complex 3jzf indicates that the complex reaches stability at 5 ns and remained stable till 35 ns after that there was a little increase in RMD of ligand but again it becomes stable with protein. The complexity of the RMSD plot for the given 3jzi shows that it achieves stabilization about 30 ns. However, the RMSD for the ligand is quite high, indicating a poor interaction. After then, an overall RMSD value of 2.0 Å, for (3jzf) and 3.0 Å, for (3jzi) remains for ligand up to 50 ns. After becoming stable, protein RMSD values vary within 1.0 Angstrom. This indicates that the ligand stayed attached to the receptor's binding site for most of the simulated time. However, there is greater variation in (3jzi) than in (3jzf). Molecular docking modeling show and verify that protein and ligand have the similar relations beside nearby residues, resulting in an outstanding match through ACCase' active site.