Abstract
Castor bean (Ricinus Communis) oil has been reported as one of the most important bio-based fuels; however, high amounts of toxic solid residue are generated in the production. This toxicity is due to several molecules, ricin protein being the most studied compound. The inhibition of the ricin protein is essential for eliminating its toxicity. The objective of this study is to predict the possible inhibition process via the interactions between the ricin protein and the flavonoids quercetin (Q) and epigallocatechin gallate (EGCG). The molecular structures of the complexes formed between the ricin protein and flavonoids were studied using quantum-chemical and molecular docking calculations to analyze the type of interaction, active site of the protein, binding energies, and different conformations in the inhibition process. Different methodologies were applied for the molecular structure determination; the best approximation was obtained with B3LYP/6-31G (d,p) theoretical methodology. Mappings of electrostatic potential (MEP) and frontier molecular orbitals were used for the identification of the probable sites of interaction, which were confirmed by molecular docking. The adjustment and alignment of flavonoid groups before and after the interaction, and charge transfer parameters, showed that Q and EGCG act as electron donors inside of the active site in ricin.
Highlights
Castor bean seeds (Ricinus Communis) have been used as an alternative source of biofuels due to the high demand that currently exists for biomass fuels
Derivatives of flavonoid groups have been analyzed by the B3LYP and M06-2X functional, determining the molecular factors of their structural and energetic properties [38,39]. These theoretical calculations can be incredibly helpful in the prediction of chemical reactivity parameters and molecular structure; the last method mentioned is used for alignment and adjustment of a ligand, which is necessary because the initial pose of a ligand in a free solution is different from the pose of the protein-bound ligand [40–42]
The results show the interactions between the active site of A chain and the ligands Q and
Summary
Mayra Cristina Martínez-Ceniceros 1 , Linda-Lucila Landeros-Martínez 1 , Nora-Aydeé Sánchez-Bojorge 1 , Fabiola Sandoval-Salas 2 , Hilda Amelia Piñón-Castillo 1 , León Raúl Hernández-Ochoa 1 and Luz María Rodríguez-Valdez 1, *.
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